Membrane Protein Topology Database
Listing generated on Friday, July 4, 2008
Created by Sajith Jayasinghe, Kalina Hristova, Stephen White
Managed and maintained by Michael Myers and Craig Snider
Copyright (c) 2000-2008 by its creators. All rights reserved.
When referring to this database, please use the following references:
S. Jayasinghe, K. Hristova, and S. H. White (2001). MPtopo: A
database of membrane protein topology. Protein Sci. 10:455-458.
http://blanco.biomol.uci.edu/mptopo
Address correspondence to:
Stephen White
University of California at Irvine
Dept. of Physiology and Biophysics
Med. Sci. I, D346
Irvine, CA 92697-4560
949-824-7122, phone
949-824-8540, fax
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The database entries are divided into three subsets:
3D_helix: helix-bundle proteins of known 3-D structure.
1D_helix: helix-bundle proteins whose topologies have been tested
experimentally.
3D_other: beta-barrel and monotopic membrane proteins of known 3-D
structure.
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>3D_helix;140
protein_name:AChR pore alpha subunit (Torpedo marmorata)
file_name:ACh_pore_alpha.txt
entry_date:3july03
refman_number:21022
endnote_number:
author:Miyazawa,A., Fujiyoshi,Y., Unwin,N.(2003) [Structure and gating mechanism of the acetylcholine receptor pore] {Nature, 423, 949-955}
remarks:Sequence is from PDB, chain A. There is additional 24 AA as signal sequence in Swiss-Prot. TMhelices=4.
pir_number:
Swiss_Prot_entry:ACHA_TORMA
Swiss_Prot_number:P02711
Swiss_Prot_gene:CHRNA1
Swiss_Prot_name:Acetylcholine receptor subunit alpha
PDB_title:Acetylcholine Receptor Protein, alpha Chain
PDB_Identifier:1OED
N_terminal:in
number_tmsegs:4
tm_segments:A.211,237;B.243,271;C.275,300;D.403,436
sequence:SEHETRLVANLLENYNKVIRPVEHHTHFVDITVGLQLIQLINVDEVNQIVETNVRLRQQWIDVRLRWNPADYGGIKKIRLPSDDVWLPDLVLYNNADGDFAIVHMTKLLLDYTGKIMWTPPAIFKSYCEIIVTHFPFDQQNCTMKLGIWTYDGTKVSISPESDRPDLSTFMESGEWVMKDYRGWKHWVYYTCCPDTPYLDITYHFIMQRIPLYFVVNVIIPCLLFSFLTVLVFYLPTDSGEKMTLSISVLLSLTVFLLVIVELIPSTSSAVPLIGKYMLFTMIFVISSIIVTVVVINTHHRSPSTHTMPQWVRKIFINTIPNVMFFSTMKRASKEKQENKIFADDIDISDISGKQVTGEVIFQTPLIKNPDVKSAIEGVKYIAEHMKSDEESSNAAEEWKYVAMVIDHILLCVFMLICIIGTVSVFAGRLIELSQEG*
>3D_helix;141
protein_name:AChR pore beta subunit (Torpedo marmorata)
file_name:ACh_pore_beta.txt
entry_date:3july03
refman_number:21022
endnote_number:
author:Miyazawa,A., Fujiyoshi,Y., Unwin,N.(2003) [Structure and gating mechanism of the acetylcholine receptor pore] {Nature, 423, 949-955}
remarks:Sequence is from PDB, chain B. There is additional 24 AA as signal sequence in Swiss-Prot. TMhelices=4.
pir_number:
Swiss_Prot_entry:Q6S3I0_TORMA
Swiss_Prot_number:Q6S3I0
Swiss_Prot_gene:none
Swiss_Prot_name:Acetylcholine receptor beta subunit
PDB_title:Acetylcholine Receptor Protein, beta Chain
PDB_Identifier:1OED
N_terminal:in
number_tmsegs:4
tm_segments:A.224,241;B.249,274;C.290,306;D.438,462
sequence:SVMEDTLLSVLFENYNPKVRPSQTVGDKVTVRVGLTLTSLLILNEKNEEMTTSVFLNLAWTDYRLQWDPAAYEGIKDLSIPSDDVWQPDIVLMNNNDGSFEITLHVNVLVQHTGAVSWHPSAIYRSSCTIKVMYFPFDWQNCTMVFKSYTYDTSEVILQHALDAKGEREVKEIMINQDAFTENGQWSIEHKPSRKNWRSDDPSYEDVTFYLIIQRKPLFYIVYTIVPCILISILAILVFYLPPDAGEKMSLSISALLALTVFLLLLADKVPETSLSVPIIISYLMFIMILVAFSVILSVVVLNLHHRSPNTHTMPNWIRQIFIETLPPFLWIQRPVTTPSPDSKPTIISRANDEYFIRKPAGDFVCPVDNARVAVQPERLFSEMKWHLNGLTQPVTLPQDLKEAVEAIKYIAEQLESASEFDDLKKDWQYVAMVADRLFLYIFITMCSIGTFSIFLDASHNVPPDNPFA*
>3D_helix;143
protein_name:AChR pore delta subunit (Torpedo marmorata)
file_name:ACh_pore_delta.txt
entry_date:4dec03
refman_number:21022
endnote_number:
author:Miyazawa,A., Fujiyoshi,Y., Unwin,N.(2003) [Structure and gating mechanism of the acetylcholine receptor pore] {Nature, 423, 949-955}
remarks:Sequence is from PDB, chain C. Sequence in PDB has first 21 AA removed relative to Swiss-Prot. TMhelices=4.
pir_number:
Swiss_Prot_entry:Q6S3H8_TORMA
Swiss_Prot_number:Q6S3H8
Swiss_Prot_gene:none
Swiss_Prot_name:Acetylcholine receptor delta subunit
PDB_title:Acetylcholine Receptor Protein, delta Chain
PDB_Identifier:1OED
N_terminal:in
number_tmsegs:4
tm_segments:A.226,253;B.257,285;C.289,316;D.452,483
sequence:VNEEERLINDLLIVNKYNKHVRPVKHNNEVVNIALSLTLSNLISLKETDETLTTNVWMDHAWYDHRLTWNASEYSDISILRLRPELIWIPDIVLQNNNDGQYNVAYFCNVLVRPNGYVTWLPPAIFRSSCPINVLYFPFDWQNCSLKFTALNYNANEISMDLMTDTIDGKDYPIEWIIIDPEAFTENGEWEIIHKPAKKNIYGDKFPNGTNYQDVTFYLIIRRKPLFYVINFITPCVLISFLAALAFYLPAESGEKMSTAICVLLAQAVFLLLTSQRLPETALAVPLIGKYLMFIMSLVTGVVVNCGIVLNFHFRTPSTHVLSTRVKQIFLEKLPRILHMSRVDEIEQPDWQNDLKLRRSSSVGYISKAQEYFNIKSRSELMFEKQSERHGLVPRVTPRIGFGNNNENIAASDQLHDEIKSGIDSTNYIVKQIKEKNAYDEEVGNWNLVGQTIDRLSMFIITPVMVLGTIFIFVMGNFNRPPAKPFEGDPFDYSSDHPRCA*
>3D_helix;142
protein_name:AChR pore gamma subunit (Torpedo marmorata)
file_name:ACh_pore_gamma.txt
entry_date:4dec03
refman_number:21022
endnote_number:
author:Miyazawa,A., Fujiyoshi,Y., Unwin,N.(2003) [Structure and gating mechanism of the acetylcholine receptor pore] {Nature, 423, 949-955}
remarks:Sequence is from PDB, chain E. Sequence in PDB has first 16 AA removed relative to Swiss-Prot. TMhelices=4.
pir_number:
Swiss_Prot_entry:Q6S3H9_TORMA
Swiss_Prot_number:Q6S3H9
Swiss_Prot_gene:none
Swiss_Prot_name:Acetylcholine receptor gamma subunit
PDB_title:Acetylcholine Receptor Protein, gamma Chain
PDB_Identifier:1OED
N_terminal:in
number_tmsegs:4
tm_segments:A.221,246;B.250,280;C.286,311;D.446,478
sequence:NEEGRLIEKLLGDYDKRIKPAKTLDHVIDVTLKLTLTNLISLNEKEEALTTNVWIEIQWNDYRLSWNTSEYEGIDLVRIPSELLWLPDVVLENNVDGQFEVAYYANVLVYNDGSMYWLPPAIYRSTCPIAVTYFPFDWQNCSLVFRSQTYNAHEVNLQLSAEEGEVVEWIHIDPEDFTENGEWTIRHRPAKKNYNWQLTKDDIDFQEIIFFLIIQRKPLFYIINIIAPCVLISSLVVLVYFLPAQAGGQKCTLSISVLLAQTIFLFLIAQKVPETSLNVPLIGKYLIFVMFVSLVIVTNCVIVLNVSLRTPNTHSLSEKIKHLFLEFLPKYLGMHLEPSEETPEKPQPRRRSSFGIMIKAEEYILKKPRSELMFEEQKDRHGLKRVNKMTSDIDIGTTVDLYKDLANFAPEIKSCVEACNFIAKSTKEQNDSGSENENWVLIGKVIDKACFWIALLLFSLGTLAIFLTGHLNQVPEFPFPGDPRKYVP*
>3D_helix;116
protein_name:AcrB multidrug transporter (E. coli)
file_name:AcrB.txt
entry_date:21oct02
refman_number:20603,20969
endnote_number:
author:Murakami,S., Nakashima,R., Yamashita,E., Yamaguchi,A. (2002) [Crystal structure of bacterial multidrug efflux transporter AcrB] {Nature, 419, 587-593}
remarks:Sequence from Swiss-Prot. TMhelices=12.
pir_number:B36938
Swiss_Prot_entry:ACRB_ECOLI
Swiss_Prot_number:P31224
Swiss_Prot_gene:ACRB,ACRE,B0462
Swiss_Prot_name:Acriflavine resistance protein B
PDB_title:multidrug efflux transporter Acrb
PDB_Identifier:1IWG
N_terminal:in
number_tmsegs:12
tm_segments:A.11,29;B.331,356;C.367,386;D.395,421;E.439,457;F.465,497;G.537,557;H.873,892;I.896,919;J.925,954;K.972,990;L.999,1021
sequence:MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVDHH*
>3D_helix;133
protein_name:ADP/ATP carrier protein* (bovine)
file_name:ADP_ATP_carrier.txt
entry_date:28nov03
refman_number:21188
endnote_number:
author:Pebay-Peyroula,E., Dahout-Gonzalez,D., Kahn,R., Trézéguet,V., Lauquin,G.J.-M., Brandolin,G. (2003) [Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside] {Nature, 426, 39-44}
remarks:*The helices form a deep, broad cavity lined with polar residues. This means that some of the TM segments are quite polar. Sequence from Swiss-Prot. TMhelices=6.
pir_number:A43646,XWBO
Swiss_Prot_entry:ADT1_BOVIN
Swiss_Prot_number:P02722
Swiss_Prot_gene:SLC25A4, ANT1
Swiss_Prot_name:ADP,ATP carrier protein, heart isoform T1
PDB_title:ADP, ATP carrier protein heart isoform T1
PDB_Identifier:1OKC
N_terminal:out
number_tmsegs:6
tm_segments:A.4,37;B.73,99;C.108,142;D.176,199;E.209,238;F.273,290
sequence:SDQALSFLKDFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKGAAQREFTGLGNCITKIFKSDGLRGLYQGFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIIVSWMIAQTVTAVAGLVSYPFDTVRRRMMMQSGRKGADIMYTGTVDCWRKIAKDEGPKAFFKGAWSNVLRGMGGAFVLVLYDEIKKFV*
>3D_helix;217
protein_name:amonia transporter AmtB (E. coli)
file_name:AmtB_Ecoli.txt
entry_date:08mar05
refman_number:21592
endnote_number:
author:Khademi,S., O'Connell,J.,III, Remis,J., Robles-Colmenares,Y., Miercke,L.J.W., Stroud,R.M. (2004) [Mechanism of ammonia transport by Amt/MEP/Rh: Structure of AmtB at 1.35 Å] {Science, 305, 1587-1594}
remarks:Sequence from PDB. Swiss-Prot sequence includes signal sequence (first 22 residues). Sequence below is from PDB and does not include signal sequence, therefore res#1 corresponds to res#23 in Swiss-Prot.
pir_number:A90692, C64775, E85542
Swiss_Prot_entry:AMTB_ECOLI
Swiss_Prot_number:P69681
Swiss_Prot_gene:amtB
Swiss_Prot_name:ammonium channel
PDB_title:Crystal structure of Ammonia Channel AmtB from E.Coli
PDB_Identifier:1U7G
N_terminal:out
number_tmsegs:11
tm_segments:A.7,33;B.38,68;C.96,120;D.125,148;E.163,182;F.195,221;G.224,253;H.256,275;I.280,306;J.310,334;K.347,380
sequence:APAVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVPEEQEREGLDVNSHGENAYNA*
>3D_helix;162
protein_name:aquaporin 1* (bovine)
file_name:AQP1_bovine.txt
entry_date:10dec03
refman_number:20112
endnote_number:
author:Sui,H.X., Han,B.-G., Lee,J.K., Walian,P., Jap,B.K. (2001) [Structural basis of water-specific transport through the AQP1 water channel] {Nature, 414, 872-878}
remarks:One of the TM segments, C* + *C, is composed of two end-to-end helical segments. The two partial segments are counted as 2 TM segments topologically. Sequence is from Swiss-Prot. TMhelices=6.
pir_number:JC2348
Swiss_Prot_entry:AQP1_BOVIN
Swiss_Prot_number:P47865
Swiss_Prot_gene:AQP1
Swiss_Prot_name:Aquaporin-CHIP
PDB_title:aquaporin 1
PDB_Identifier:1J4N
N_terminal:in
number_tmsegs:8
tm_segments:A.10,34;B.51,68;C*.79,88;D.93,117;E.143,158;F.170,187;*C.194,204;G.216,230
sequence:MASEFKKKLFWRAVVAEFLAMILFIFISIGSALGFHYPIKSNQTTGAVQDNVKVSLAFGLSIATLAQSVGHISGAHLNPAVTLGLLLSCQISVLRAIMYIIAQCVGAIVATAILSGITSSLPDNSLGLNALAPGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSGPLAIGFSVALGHLLAIDYTGCGINPARSFGSSVITHNFQDHWIFWVGPFIGAALAVLIYDFILAPRSSDLTDRVKVWTSGQVEEYDLDADDINSRVEMKPK*
>3D_helix;81
protein_name:aquaporin 1* (human)
file_name:AQP1_human.txt
entry_date:3mar00
refman_number:19204
endnote_number:
author:Murata,K. Mitsuoka,K. Hirai,T. Walz,T. Agre,P. Heymann,J.B. Engel,A. Fujiyoshi,Y. (2000) [Structural determinants of water permeation through aquaporin-1] {Nature, 407, 599-605}
remarks:One of the TM segments, C* + *C, is composed of two end-to-end helical segments. The two partial segments are counted as 2 TM segments topologically. Sequence is from Swiss-Prot. TMhelices=6.
pir_number:A41616
Swiss_Prot_entry:AQP1_HUMAN
Swiss_Prot_number:P29972
Swiss_Prot_gene:AQP1,CHIP28
Swiss_Prot_name:Aquaporin-CHIP
PDB_title:aquaporin-1, chain A
PDB_Identifier:1FQY
N_terminal:in
number_tmsegs:8
tm_segments:A.8,36;B.49,66;C*.77,84;D.95,115;E.137,155;F.167,183;*C.193,200;G.208,228
sequence:MASEFKKKLFWRAVVAEFLATTLFVFISIGSALGFKYPVGNNQTAVQDNVKVSLAFGLSIATLAQSVGHISGAHLNPAVTLGLLLSCQISIFRALMYIIAQCVGAIVATAILSGITSSLTGNSLGRNDLADGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSAPLAIGLSVALGHLLAIDYTGCGINPARSFGSAVITHNFSNHWIFWVGPFIGGALAVLIYDFILAPRSSDLTDRVKVWTSGQVEEYDLDADDINSRVEMKPK*
>3D_helix;178
protein_name:aquaporin Z* (E. coli)
file_name:AqpZ.txt
entry_date:12jan04
refman_number:21274
endnote_number:
author:Savage,D.F., Egea,P.F., Robles-Colmenares,Y., O'Connell,J.D.,III, Stroud,R.M. (2003) [Architecture and selectivity in aquaporins: 2.5 Å x-ray structure of aquaporin Z] {PLoS Biology, 3, 334-340}
remarks:One of the TM segments, C* + *C, is composed of two end-to-end helical segments. The two partial segments are counted as 2 TM segments topologically. Sequence is from Swiss-Prot. TMhelices=6.
pir_number:C64826
Swiss_Prot_entry:AQPZ_ECOLI
Swiss_Prot_number:P48838
Swiss_Prot_gene:AQPZ,BNIP,B0875,C1009,SF0832,S0873
Swiss_Prot_name:Aquaporin Z
PDB_title:aquaporin Z
PDB_Identifier:1RC2
N_terminal:in
number_tmsegs:8
tm_segments:A.3,26;B.34,54;C*.63,73;D.79,104;E.130,154;F.161,182;*C.186,198;G.206,225
sequence:MFRKLAAECFGTFWLVFGGCGSAVLAAGFPELGIGFAGVALAFGLTVLTMAFAVGHISGGHFNPAVTIGLWAGGRFPAKEVVGYVIAQVVGGIVAAALLYLIASGKTGFDAAASGFASNGYGEHSPGGYSMLSALVVELVLSAGFLLVIHGATDKFAPAGFAPIAIGLALTLIHLISIPVTNTSVNPARSTAVAIFQGGWALEQLWFFWVVPIVGGIIGGLIYRTLLEKRD*
>3D_helix;29
protein_name:bacteriorhodopsin (H. salinarium)
file_name:bR.txt
entry_date:27may98
refman_number:17666
endnote_number:
author:Luecke,H., Schobert,B., Richter,H.-T., Cartailler,J.-P., Lanyi,J.K. (1999) [Structure of bacteriorhodopsin at 1.55 Å resolution] {J Mol Biol, 291, 899-911}
remarks:Sequence below is processed sequence from Swiss-Prot (13 AA signal sequence removed). TMhelices=7.
pir_number:RAHSB
Swiss_Prot_entry:BACR_HALSA
Swiss_Prot_number:P02945
Swiss_Prot_gene:bop
Swiss_Prot_name:Bacteriorhodopsin [Precursor]
PDB_title:bacteriorhodopsin
PDB_Identifier:1BRX,2BRD,1AP9,1AT9,1BRD
N_terminal:out
number_tmsegs:7
tm_segments:A.9,31;B.36,63;C.81,101;D.104,127;E.133,155;F.164,192;G.200,225
sequence:QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSAGDGAAATSD*
>3D_helix;109
protein_name:BtuCD ABC transporter, BtuC subunit (Escherichia coli)
file_name:ABC-transporter_BtuC.txt
entry_date:6Aug02
refman_number:20289
endnote_number:
author:Locher,K.P., Lee,A.T., Rees,D.C. (2002) [The E. coli BtuCD structure: A framework for ABC transporter architecture and mechanism] {Science, 296, 1091-1098}
remarks:TM helix G does not cross the membrane completely. It ends in an extended stretch packed between several other helices. Functional protein has 2 BtuC subunits (membrane spanning) & 2 BtuD subunits. Not all TM segments are fully helical. Sequence from Swiss-Prot. TMhelices=10.
pir_number:B90931
Swiss_Prot_entry:BTUC_ECO57
Swiss_Prot_number:Q8X4L7
Swiss_Prot_gene:BTUC,Z2740,ECS2418
Swiss_Prot_name:Vitamin B12 transport system permease protein btuC
PDB_title:bacterial ABC transporter involved in B12 uptake
PDB_Identifier:1L7V
N_terminal:in
number_tmsegs:10
tm_segments:A.2,32;B.47,81;C.93,107;D.114,138;E.142,166;F.191,206;G.229,249;H.258,267;I.272,296;J.305,324
sequence:MLTLARQQQRQNIRWLLCLSVLMLLALLLSLCAGEQWISPGDWFSPRGELFVWQIRLPRTLAVLLVGAALAISGAVMQALFENPLAEPGLLGVSNGAGVGLIAAVLLGQGQLPNWALGLCAIAGALIITLILLRFARRHLSTSRLLLAGVALGIICSALMTWAIYFSTSVDLRQLMYWMMGGFGGVDWRQSWLMLALIPMLLWICCQSRPMNMLALGEISARQLGLPLWFWRNVLVAATGWMVGVSVALAGAIGFIGLVIPHILRLCGLTDHRALLPGCALAGASALLLADIVARLALAAAELPIGVVTATLGAPVFIWLLLKAGR*
>3D_helix;83
protein_name:Ca ATPase, SR (rabbit)
file_name:CaATPase_SR_r.txt
entry_date:20Jun00
refman_number:18872
endnote_number:
author:Toyoshima,C., Nakasako,M., Nomura,H., and Ogawa,H. (2000) [Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution] {Nature, 405, 647-655}
remarks:helix E protrudes into a soluble domain. Nterm in = cytoplasm, out = SR lumen. Sequence is from Swiss-Prot. PDB sequence is C-terminus truncated/modified. TMhelices=10.
pir_number:PWRBFC
Swiss_Prot_entry:ATA1_RABIT
Swiss_Prot_number:P04191
Swiss_Prot_gene:ATP2A1
Swiss_Prot_name:Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
PDB_title:Calcium-Transporting ATPase Sarcoplasmic Reticulum Type, Fast Twitch Skeletal Muscle, Adult Isoform, Chain A
PDB_Identifier:1EUL
N_terminal:in
number_tmsegs:10
tm_segments:A.48,80;B.89,119;C.247,274;D.289,307;E.739,779;F.788,809;G.830,852;H.893,912;I.930,950;J.964,986
sequence:MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALKEYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMAATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMKKEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGMLDPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAMGSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAIGGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLKALDLTQWLMVLKISLPVIGLDEILKFIARNYLEDPEDERRK*
>3D_helix;176
protein_name:ClC chloride channel* (E. coli)
file_name:ClC_Ecoli.txt
entry_date:1jan04
refman_number:20087,20550,20975
endnote_number:
author:Dutzler,R., Campbell,E.B., Cadene,M., Chait,B.T., MacKinnon,R. (2002) [X-ray structure of a CIC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity] {Nature, 415, 287-294}
remarks:*The topology of this protein is complex! The 'tmsegs' are all helical segments buried within the protein and membrane. Check original papers for details. Sequence is from Swiss-Prot. TMhelices=14 (based on turn reversals).
pir_number:C64739
Swiss_Prot_entry:CLCA_ECOLI
Swiss_Prot_number:P37019
Swiss_Prot_gene:CLCA,ERIC,B0155
Swiss_Prot_name:Voltage-gated ClC-type chloride channel clcA
PDB_title:ClC chloride channel
PDB_Identifier:1KPK,1OTS
N_terminal:in
number_tmsegs:17
tm_segments:A.33,70;B.77,99;C.108,116;D.123,141;E.148,166;F.171,189;G.193,203;H.213,233;I.254,283;J.288,306;K.320,323;L.329,350;M.356,377;N.386,402;O.404,416;P.421,439;Q.442,458
sequence:MKTDTPSLETPQAARLRRRQLIRQLLERDKTPLAILFMAAVVGTLVGLAAVAFDKGVAWLQNQRMGALVHTADNYPLLLTVAFLCSAVLAMFGYFLVRKYAPEAGGSGIPEIEGALEDQRPVRWWRVLPVKFFGGLGTLGGGMVLGREGPTVQIGGNIGRMVLDIFRLKGDEARHTLLATGAAAGLAAAFNAPLAGILFIIEEMRPQFRYTLISIKAVFIGVIMSTIMYRIFNHEVALIDVGKLSDAPLNTLWLYLILGIIFGIFGPIFNKWVLGMQDLLHRVHGGNITKWVLMGGAIGGLCGLLGFVAPATSGGGFNLIPIATAGNFSMGMLVFIFVARVITTLLCFSSGAPGGIFAPMLALGTVLGTAFGMVAVELFPQYHLEAGTFAIAGMGALLAASIRAPLTGIILVLEMTDNYQLILPMIITGLGATLLAQFTGGKPLYSAILARTLAKQEAEQLARSKAASASENT*
>3D_helix;114
protein_name:ClC chloride channel* (S. typhimurium)
file_name:ClC_Styph.txt
entry_date:6Aug02
refman_number:20087
endnote_number:
author:Dutzler,R., Campbell,E.B., Cadene,M., Chait,B.T., MacKinnon,R. (2002) [X-ray structure of a CIC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity] {Nature, 415, 287-294}
remarks:*The topology of this protein is complex! The 'tmsegs' are all helical segments buried witin the protein and membrane. Check original papers for details. Sequence is from Swiss-Prot. TMhelices=14 (based on turn reversals).
pir_number:
Swiss_Prot_entry:CLCA_SALTY
Swiss_Prot_number:Q8ZRP8
Swiss_Prot_gene:CLCA,ERIC,STM0203
Swiss_Prot_name:Voltage-gated ClC-type chloride channel clcA
PDB_title:ClC chloride channel
PDB_Identifier:1KPL
N_terminal:in
number_tmsegs:17
tm_segments:A.33,70;B.77,99;C.108,116;D.123,141;E.148,166;F.171,189;G.193,203;H.213,233;I.254,283;J.288,306;K.320,323;L.329,350;M.356,377;N.386,402;O.404,416;P.421,439;Q.442,458
sequence:MKTDTSTFLAQQIVRLRRRDQIRRLMQRDKTPLAILFMAAVVGTLTGLVGVAFEKAVSWVQNMRIGALVQVADHAFLLWPLAFILSALLAMVGYFLVRKFAPEAGGSGIPEIEGALEELRPVRWWRVLPVKFIGGMGTLGAGMVLGREGPTVQIGGNLGRMVLDVFRMRSAEARHTLLATGAAAGLSAAFNAPLAGILFIIEEMRPQFRYNLISIKAVFTGVIMSSIVFRIFNGEAPIIEVGKLSDAPVNTLWLYLILGIIFGCVGPVFNSLVLRTQDMFQRFHGGEIKKWVLMGGAIGGLCGILGLIEPAAAGGGFNLIPIAAAGNFSVGLLLFIFITRVVTTLLCFSSGAPGGIFAPMLALGTLLGTAFGMAAAVLFPQYHLEAGTFAIAGMGALMAASVRAPLTGIVLVLEMTDNYQLILPMIITCLGATLLAQFLGGKPLYSTILARTLAKQDAEQAEKNQNAPADENT*
>3D_helix;255
protein_name:CorA Mg2+ transporter (Thermotoga maritima)
file_name:Magnesium_transporter_CorA_Tmaritima.txt
entry_date:29jan07
refman_number:
endnote_number:22000
author:Lunin, V.V., Dobrovetsky,E., Khutoreskaya,G., Zhang,R., Joachimiak,A., Doyle,D.A., Bochkarev,A., Maguire,M.E., Edwards,A.M., Koth, C.M.(2006) [Crystal structure of the CorA Mg2+ transporter] {Nature, 440, 833-837}
remarks:Pentameric form. Sequence for monomer from PDB. See also later structure 2IUB.
pir_number:H72360
Swiss_Prot_entry:CORA_THEMA
Swiss_Prot_number:Q9WZ31
Swiss_Prot_gene:corA
Swiss_Prot_name:Magnesium transport protein corA
PDB_title:X-ray structure of T. maritima CorA soluble domain
PDB_Identifier:2BBH
N_terminal:in
number_tmsegs:2
tm_segments:A.291,312;B.326,345
sequence:MEEKRLSAKKGLPPGTLVYTGKYREDFEIEVMNYSIEEFREFKTTDVESVLPFRDSSTPTWINITGIHRTDVVQRVGEFFGIHPLVLEDILNVHQRPKVEFFENYVFIVLKMFTYDKNLHELESEQVSLILTKNCVLMFQEKIGDVFDPVRERIRYNRGIIRKKRADYLLYSLIDALVDDYFVLLEKIDDEIDVLEEEVLERPEKETVQRTHQLKRNLVELRKTIWPLREVLSSLYRDVPPLIEKETVPYFRDVYDHTIQIADTVETFRDIVSGLLDVYLSSVSNKTNEVMKVLTIIATIFMPLTFIAGIYGMNFEYMPELRWKWGYPVVLAVMGVIAVIMVVYFKKKKWL*
>3D_helix;251
protein_name:Cysteine Oxidase DsbB (Escherichia coli)
file_name:DsbB_Ecoli.txt
entry_date:29jan07
refman_number:
endnote_number:22292
author:Inaba, K., Murakami,S., Suzuki,M., Nakagawa,A., Yamashita,E., Okada,K., Ito,K.(2006) [Crystal structure of the DsbB-DsbA complex reveals a mechanism of disulfide bond generation] {Cell, 127, 789-801}
remarks:Sequence from Swiss-Prot. This corresponds to chain B in PDB file.
pir_number:F64864
Swiss_Prot_entry:DSBB_ECOLI
Swiss_Prot_number:P0A6M2
Swiss_Prot_gene:dsbB
Swiss_Prot_name:Disulfide bond formation protein B
PDB_title:Crystal structure of DsbA-DsbB-ubiquinone complex
PDB_Identifier:2HI7
N_terminal:in
number_tmsegs:4
tm_segments:A.15,36;B.46,65;C.72,93;D.145,163
sequence:MLRFLNQCSQGRGAWLLMAFTALALELTALWFQHVMLLKPCVLCIYERCALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVISQPFKAKKRDLFGR*
>3D_helix;146
protein_name:cyt. b6f complex, cyto b6 subunit (Mastigocladus laminosus)
file_name:cytob6f_b6_Mastlam.txt
entry_date:4dec03
refman_number:21201
endnote_number:
author:Kurisu,G., Zhang,H., Smith,J.L., Cramer,W.A. (2003) [Structure of the cytochrome b6f complex of oxygenic photosynthesis: Tuning the cavity] {Science, 302, 1009-1014}
remarks:Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=4.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Cytochrome B6, Chain A
PDB_Identifier:1UM3
N_terminal:out
number_tmsegs:4
tm_segments:A.34,55;B.79,109;C.116,137;D.178,205
sequence:MANVYDWFQERLEIQALADDVTSKYVPPHVNIFYCLGGITLTCFLIQFATGFAMTFYYKPTVTEAYASVQYIMNEVSFGWLIRSIHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWISGVILAVITVSFGVTGYSLPWDQVGYWAVKIVSGVPEAIPVVGVLISDLLRGGSSVGQATLTRYYSAHTFVLPWLIAVFMLLHFLMIRKQGISGPL*
>3D_helix;148
protein_name:cyt. b6f complex, cytochrome f (Mastigocladus laminosus)
file_name:cytob6f_cytochrome_f_Mastlam.txt
entry_date:4dec03
refman_number:21201
endnote_number:
author:Kurisu,G., Zhang,H., Smith,J.L., Cramer,W.A. (2003) [Structure of the cytochrome b6f complex of oxygenic photosynthesis: Tuning the cavity] {Science, 302, 1009-1014}
remarks:Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:cytochrome f, chain C
PDB_Identifier:1UM3
N_terminal:in
number_tmsegs:1
tm_segments:A.252,279
sequence:YPFWAQQTYPPTPREPTGRIVCANCHLAAKPAEVEVPQSVLPDTVFKAVVKIPYDTKLQQVAADGSKVGLNVGAVLMLPEGFKIAPEERIPEELKKEVGDVYFQPYKEGQDNVLLVGPLPGEQYQEIVFPVLSPNPTTDKNIHFGKYAIHLGANRGRGQIYPTGEKSNNNVFTASATGTITKIAKEEDEYGNVKYQVSIQTDSGKTVVDTIPAGPELIVSEGQAVKAGEALTNNPNVGGFGQDDTEIVLQDPNRVKWMIAFICLVMLAQLMLILKKKQVEKVQAAEMNF*
>3D_helix;152
protein_name:cyt. b6f complex, PetG (Mastigocladus laminosus)
file_name:cytob6f_PetG_Mastlam.txt
entry_date:4dec03
refman_number:21201
endnote_number:
author:Kurisu,G., Zhang,H., Smith,J.L., Cramer,W.A. (2003) [Structure of the cytochrome b6f complex of oxygenic photosynthesis: Tuning the cavity] {Science, 302, 1009-1014}
remarks:Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Pet G, Chain G
PDB_Identifier:1UM3
N_terminal:in
number_tmsegs:1
tm_segments:A.9,31
sequence:MVEPLLDGLVLGLVFATLGGLFYAAYQQYKRPNELGG*
>3D_helix;150
protein_name:cyt. b6f complex, PetL (Mastigocladus laminosus)
file_name:cytob6f_PetL_Mastlam.txt
entry_date:4dec03
refman_number:21201
endnote_number:
author:Kurisu,G., Zhang,H., Smith,J.L., Cramer,W.A. (2003) [Structure of the cytochrome b6f complex of oxygenic photosynthesis: Tuning the cavity] {Science, 302, 1009-1014}
remarks:Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Pet L, chain E
PDB_Identifier:1UM3
N_terminal:in
number_tmsegs:1
tm_segments:A.1,25
sequence:MILGAVFYIVFIALFFGIAVGIIFAIKSIKLI*
>3D_helix;151
protein_name:cyt. b6f complex, PetM (Mastigocladus laminosus)
file_name:cytob6f_PetM_Mastlam.txt
entry_date:4dec03
refman_number:21201
endnote_number:
author:Kurisu,G., Zhang,H., Smith,J.L., Cramer,W.A. (2003) [Structure of the cytochrome b6f complex of oxygenic photosynthesis: Tuning the cavity] {Science, 302, 1009-1014}
remarks:Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Pet M, chain F
PDB_Identifier:1UM3
N_terminal:in
number_tmsegs:1
tm_segments:A.2,30
sequence:MTEEMLYAALLSFGLIFVGWGLGVLLLKIQGAEKE*
>3D_helix;153
protein_name:cyt. b6f complex, PetN (Mastigocladus laminosus)
file_name:cytob6f_PetN_Mastlam.txt
entry_date:4dec03
refman_number:21201
endnote_number:
author:Kurisu,G., Zhang,H., Smith,J.L., Cramer,W.A. (2003) [Structure of the cytochrome b6f complex of oxygenic photosynthesis: Tuning the cavity] {Science, 302, 1009-1014}
remarks:Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Pet N, chain H
PDB_Identifier:1UM3
N_terminal:in
number_tmsegs:1
tm_segments:A.3,29
sequence:MEIDVLGWVALLVVFTWSIAMVVWGRNGL*
>3D_helix;149
protein_name:cyt. b6f complex, Rieske iron-sulfur protein (Mastigocladus laminosus)
file_name:cytob6f_ISP_Mastlam.txt
entry_date:4dec03
refman_number:21201
endnote_number:
author:Kurisu,G., Zhang,H., Smith,J.L., Cramer,W.A. (2003) [Structure of the cytochrome b6f complex of oxygenic photosynthesis: Tuning the cavity] {Science, 302, 1009-1014}
remarks:Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=1.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Rieske iron-sulfur protein, chain D
PDB_Identifier:1UM3
N_terminal:out
number_tmsegs:1
tm_segments:A.19,43
sequence:MAQFTESMDVPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPPSGGAVGGGTTAKDKLGNNVKVSKFLESHNAGDRVLVQGLKGDPTYIVVESKEAIRDYGINAVCTHLGCVVPWNAAENKFKCPCHGSQYDETGRVIRGPAPLSLALCHATVQDDNIVLTPWTETDFRTGEKPWWV*
>3D_helix;147
protein_name:cyt. b6f complex, subunit IV (Mastigocladus laminosus)
file_name:cytob6f_subunitIV_Mastlam.txt
entry_date:4dec03
refman_number:21201
endnote_number:
author:Kurisu,G., Zhang,H., Smith,J.L., Cramer,W.A. (2003) [Structure of the cytochrome b6f complex of oxygenic photosynthesis: Tuning the cavity] {Science, 302, 1009-1014}
remarks:Sequence is from PDB. Thylakoid lumen is defined as 'in'. TMhelices=3.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Subunit IV, chain B
PDB_Identifier:1UM3
N_terminal:out
number_tmsegs:3
tm_segments:A.35,59;B.97,115;C.127,145
sequence:MATLKKPDLSDPKLRAKLAKGMGHNYYGEPAWPNDLLYVFPVVIMGTFACIVALSVLDPAMVGEPANPFATPLEILPEWYLYPVFQILRSLPNKLLGVLLMASVPLGLILVPFIENVNKFQNPFRRPVATTIFLFGTLVTIWLGIGAALPLDKTLTLGLF*
>3D_helix;49
protein_name:cyto C oxidase. Subunit VIIb (bovine)
file_name:COX-bov-VIIb.txt
entry_date:8jun98
refman_number:8424,7153
endnote_number:
author:Tsukihara,T., Aoyama,H., Yamashita,E., Tomizaki,T., Yamaguchi,H., Shinzawa-Itoh,K., Nakashima,R., Yaono,R., Yoshikawa,S. (1996) [The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å] {Science, 272, 1136-1144}
remarks:Chain K in PDB file. Nterm in = matrix. Sequence is processed sequence from Swiss-Prot (24 AA signal sequence removed). TMhelices=1.
pir_number:OSBO7B
Swiss_Prot_entry:COX7B_BOVIN
Swiss_Prot_number:P13183
Swiss_Prot_gene:COX7B
Swiss_Prot_name:Cytochrome c oxidase polypeptide VIIb, mitochondrial [Precursor]
PDB_title:cytochrome c oxidase
PDB_Identifier:1OCC
N_terminal:in
number_tmsegs:1
tm_segments:A.9,35
sequence:IHQKRAPDFHDKYGNAVLASGATFCVAVWVYMATQIGIEWNPSPVGRVTPKEWREQ*
>3D_helix;57
protein_name:cyto. bc1 complex. Chain C (bovine)
file_name:BC1-bov-C.txt
entry_date:07oct98
refman_number:16273,13829,15150
endnote_number:
author:Iwata,S., Lee,J.W., Okada,K., Lee,J.K., Iwata,M., Rasmussen,B., Link,T.A., Ramaswamy,S., Jap,B.K. (1998) [Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex] {Science, 281, 64-71}
remarks:Chain designation is that of PDB. Corresponds to cytochrome b in cited paper. Matrix = in. TMhelices=8.
pir_number:CBBO
Swiss_Prot_entry:CYB_BOVIN
Swiss_Prot_number:P00157
Swiss_Prot_gene:MTCYB,COB,CYTB
Swiss_Prot_name:Cytochrome b
PDB_title:Cytochrome Bc1 Complex from Bovine
PDB_Identifier:1BGY,1QCR,1BCC
N_terminal:in
number_tmsegs:8
tm_segments:A.29,53;B.76,104;C.110,133;D.172,202;E.224,245;F.287,307;G.319,340;H.345,376
sequence:MTNIRKSHPLMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTTTAFSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILLLTVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFAFHFILPFIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALMLLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILILALIPLLHTSKQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFLLILVLMPTAGTIENKLLKW*
>3D_helix;58
protein_name:cyto. bc1 complex. Chain D (bovine)
file_name:BC1-bov-D.txt
entry_date:07oct98
refman_number:16273,13829,15150
endnote_number:
author:Iwata,S., Lee,J.W., Okada,K., Lee,J.K., Iwata,M., Rasmussen,B., Link,T.A., Ramaswamy,S., Jap,B.K. (1998) [Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex] {Science, 281, 64-71}
remarks:Chain designation is that of PDB. Corresponds to cytochrome C1 in cited paper. Matrix = in. TMhelices=1.
pir_number:CCBO1
Swiss_Prot_entry:CY1_BOVIN
Swiss_Prot_number:P00125
Swiss_Prot_gene:CYC1
Swiss_Prot_name:Cytochrome c1, heme protein, mitochondrial
PDB_title:Cytochrome Bc1 Complex from Bovine
PDB_Identifier:1BGY,1QCR,1BCC
N_terminal:out
number_tmsegs:1
tm_segments:A.197,232
sequence:SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLVGVCYTEDEAKALAEEVEVQDGPNEDGEMFMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRARHGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQAIGMAPPIYNEVLEFDDGTPATMSQVAKDVCTFLRWAAEPEHDHRKRMGLKMLLMMGLLLPLVYAMKRHKWSVLKSRKLAYRPPK*
>3D_helix;107
protein_name:cyto. bc1 complex. Chain E (bovine)
file_name:BC1-bov-E.txt
entry_date:19Nov01
refman_number:16273,13829,15150
endnote_number:
author:Iwata,S., Lee,J.W., Okada,K., Lee,J.K., Iwata,M., Rasmussen,B., Link,T.A., Ramaswamy,S., Jap,B.K. (1998) [Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex] {Science, 281, 64-71}
remarks:Chain designation is that of PDB. Sequence from PDB, which is highly truncated, at both ends, relative to Swiss-Prot. Corresponds to Rieske protein TM domain. Matrix = in. TMhelices=1.
pir_number:A34660
Swiss_Prot_entry:UCRI_BOVIN
Swiss_Prot_number:P13272
Swiss_Prot_gene:UQCRFS1
Swiss_Prot_name:Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial [Precursor]
PDB_title:Cytochrome Bc1 Complex from Bovine
PDB_Identifier:1BGY,1QCR,1BCC
N_terminal:in
number_tmsegs:1
tm_segments:A.31,61
sequence:SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNLEVPSYEFTSDDMVIVG*
>3D_helix;59
protein_name:cyto. bc1 complex. Chain G (bovine)
file_name:BC1-bov-G.txt
entry_date:07oct98
refman_number:16273,13829,15150
endnote_number:
author:Iwata,S., Lee,J.W., Okada,K., Lee,J.K., Iwata,M., Rasmussen,B., Link,T.A., Ramaswamy,S., Jap,B.K. (1998) [Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex] {Science, 281, 64-71}
remarks:Chain designation is that of PDB. Corresponds to subunit 7 of cited reference. Sequence also from PDB file. PIR sequence differs in one position from the PDB and Swiss-Prot sequence. Matrix = in. TMhelices=1.
pir_number:A24864
Swiss_Prot_entry:UCRQ_BOVIN
Swiss_Prot_number:P13271
Swiss_Prot_gene:
Swiss_Prot_name:Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
PDB_title:Cytochrome Bc1 Complex from Bovine - chain G
PDB_Identifier:1BGY,1QCR,1BCC
N_terminal:in
number_tmsegs:1
tm_segments:A.29,71
sequence:GRQFGHLTRVRHLITYSLSPFEQRPFPHYFSKGVPNVWRRLRACILRVAPPFLAFYLLYTWGTQEFEKSKRKNPAAYVNDR*
>3D_helix;60
protein_name:cyto. bc1 complex. Chain J (bovine)
file_name:BC1-bov-J.txt
entry_date:07oct98
refman_number:16273,13829,15150
endnote_number:
author:Iwata,S., Lee,J.W., Okada,K., Lee,J.K., Iwata,M., Rasmussen,B., Link,T.A., Ramaswamy,S., Jap,B.K. (1998) [Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex] {Science, 281, 64-71}
remarks:Chain designation is that of PDB. Corresponds to subunit 10 in cited paper. Sequence also from PDB file. PIR sequence equal in length but differs in one residue. Matrix = in. TMhelices=1.
pir_number:CCBO17
Swiss_Prot_entry:UCRX_BOVIN
Swiss_Prot_number:P00130
Swiss_Prot_gene:
Swiss_Prot_name:Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
PDB_title:Cytochrome Bc1 Complex from Bovine
PDB_Identifier:1BGY,1QCR,1BCC
N_terminal:in
number_tmsegs:1
tm_segments:A.17,48
sequence:VAPTLTARLYSLLFRRTSTFALTIVVGALLFERAFDQGADAIYEHINEGKLWKHIKHKYENK*
>3D_helix;61
protein_name:cyto. bc1 complex. Chain K (bovine)
file_name:BC1-bov-K.txt
entry_date:07oct98
refman_number:16273,13829,15150
endnote_number:
author:Iwata,S., Lee,J.W., Okada,K., Lee,J.K., Iwata,M., Rasmussen,B., Link,T.A., Ramaswamy,S., Jap,B.K. (1998) [Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex] {Science, 281, 64-71}
remarks:Chain designation is that of PDB. Corresponds to subunit II in cited paper. Sequence also from PDB file. PDB and PIR are identical, but the Swiss-Prot sequence differs in 3 positions, 2 in the TM domain. Matrix = in. TMhelices=1.
pir_number:CBBOC6
Swiss_Prot_entry:UCRY_BOVIN
Swiss_Prot_number:P07552
Swiss_Prot_gene:
Swiss_Prot_name:Ubiquinol-cytochrome C reductase complex 6.4 kDa protein
PDB_title:Cytochrome Bc1 Complex from Bovine
PDB_Identifier:1BGY,1QCR,1BCC
N_terminal:in
number_tmsegs:1
tm_segments:A.17,35
sequence:MLTRFLGPRYRQLARNWVPTAQLWGAVGAVGLVSATDSRLILDWVPYINGKFKKDD*
>3D_helix;42
protein_name:cyto. C oxidase. Subunit I (bovine)
file_name:COX-bov-I.txt
entry_date:8jun98
refman_number:8424,7153
endnote_number:
author:Tsukihara,T., Aoyama,H., Yamashita,E., Tomizaki,T., Yamaguchi,H., Shinzawa-Itoh,K., Nakashima,R., Yaono,R., Yoshikawa,S. (1996) [The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å] {Science, 272, 1136-1144}
remarks:Chain A in PDB file. Nterm in = matrix. Sequence from Swiss-Prot. TMhelices=12.
pir_number:ODBO1
Swiss_Prot_entry:COX1_BOVIN
Swiss_Prot_number:P00396
Swiss_Prot_gene:MTCO1,COI
Swiss_Prot_name:Cytochrome c oxidase polypeptide I
PDB_title:cytochrome c oxidase
PDB_Identifier:1OCC
N_terminal:in
number_tmsegs:12
tm_segments:A.12,40;B.51,86;C.95,117;D.141,170;E.183,212;F.238,261;G.270,286;H.299,327;I.336,357;J.371,400;K.407,433;L.447,478
sequence:MFINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIHFAIMFVGVNMTFFPQHFLGLSGMPRRYSDYPDAYTMWNTISSMGSFISLTAVMLMVFIIWEAFASKREVLTVDLTTTNLEWLNGCPPPYHTFEEPTYVNLK*
>3D_helix;67
protein_name:cyto. C oxidase. Subunit I (P. denitrificans)
file_name:COX-para-I.txt
entry_date:12oct98
refman_number:7109,19016
endnote_number:
author:Iwata,S., Ostermeier,C., Ludwig,B., Michel,H. (1995) [Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans] {Nature, 376, 660-669}
remarks:Chain A in PDB file. See also J. Biol. Chem. (1999) 274:33296-33299. Sequence from Swiss-Prot. TMhelices=12.
pir_number:S08270
Swiss_Prot_entry:CX1B_PARDE
Swiss_Prot_number:P98002
Swiss_Prot_gene:CTADII
Swiss_Prot_name:Cytochrome c oxidase polypeptide I-beta
PDB_title:Cytochrome C Oxidase Polypeptide I-Beta
PDB_Identifier:1QLE
N_terminal:in
number_tmsegs:12
tm_segments:A.27,59;B.84,121;C.130,151;D.178,206;E.218,251;F.263,298;G.304,322;H.334,362;I.370,395;J.404,430;K.441,468;L.483,513
sequence:MADAAVHGHGDHHDTRGFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMCLEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVLYPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNYWNEHADTLEWTLPSPPPEHTFETLPKREDWDRAHAH*
>3D_helix;43
protein_name:cyto. C oxidase. Subunit II (bovine)
file_name:COX-bov-II.txt
entry_date:8jun98
refman_number:8424,7153
endnote_number:
author:Tsukihara,T., Aoyama,H., Yamashita,E., Tomizaki,T., Yamaguchi,H., Shinzawa-Itoh,K., Nakashima,R., Yaono,R., Yoshikawa,S. (1996) [The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å] {Science, 272, 1136-1144}
remarks:Chain B in PDB file. Nterm in = matrix. Sequence from Swiss-Prot. TMhelices=2.
pir_number:OBBO2
Swiss_Prot_entry:COX2_BOVIN
Swiss_Prot_number:P00404
Swiss_Prot_gene:MTCO2,COII
Swiss_Prot_name:Cytochrome c oxidase polypeptide II
PDB_title:cytochrome c oxidase
PDB_Identifier:1OCC
N_terminal:out
number_tmsegs:2
tm_segments:A.15,45;B.60,87
sequence:MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML*
>3D_helix;68
protein_name:cyto. C oxidase. Subunit II (P. denitrificans)
file_name:COX-para-II.txt
entry_date:12oct98
refman_number:7109,19016
endnote_number:
author:Iwata,S., Ostermeier,C., Ludwig,B., Michel,H. (1995) [Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans] {Nature, 376, 660-669}
remarks:Chain B in PDB file. See also J.Biol.Chem. (1999) 274:33296-33299. Nterm in = cytoplasm. Sequence is processed sequence from Swiss-Prot (29 AA signal sequence removed). TMhelices=2.
pir_number:
Swiss_Prot_entry:COX2_PARDE
Swiss_Prot_number:P08306
Swiss_Prot_gene:CTAC,CTAB,COII
Swiss_Prot_name:Cytochrome c oxidase polypeptide II [Precursor]
PDB_title:Cytochrome C Oxidase Polypeptide II
PDB_Identifier:1QLE
N_terminal:out
number_tmsegs:2
tm_segments:A.27,59;B.74,105
sequence:QDVLGDLPVIGKPVNGGMNFQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVIWTLVPVLILVAIGAFSLPILFRSQEMPNDPDLVIKAIGHQWYWSYEYPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIPAFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGAKEEFAADASDYLPASPVKLASAE*
>3D_helix;44
protein_name:cyto. C oxidase. Subunit III (bovine)
file_name:COX-bov-III.txt
entry_date:8jun98
refman_number:8424,7153
endnote_number:
author:Tsukihara,T., Aoyama,H., Yamashita,E., Tomizaki,T., Yamaguchi,H., Shinzawa-Itoh,K., Nakashima,R., Yaono,R., Yoshikawa,S. (1996) [The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å] {Science, 272, 1136-1144}
remarks:Chain C in PDB file. Nterm in = matrix. Sequence from Swiss-Prot. TMhelices=7.
pir_number:OTBO3
Swiss_Prot_entry:COX3_BOVIN
Swiss_Prot_number:P00415
Swiss_Prot_gene:MTCO3,COIII
Swiss_Prot_name:Cytochrome c oxidase polypeptide III
PDB_title:cytochrome c oxidase
PDB_Identifier:1OCC
N_terminal:in
number_tmsegs:7
tm_segments:A.16,34;B.41,66;C.73,105;D.129,152;E.156,183;F.191,223;G.233,256
sequence:MTHQTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHFNSMTLLMIGLTTNMLTMYQWWRDVIRESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLNTSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYEAPFTISDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAGAWYWHFVDVVWLFLYVSIYWWGS*
>3D_helix;72
protein_name:cyto. C oxidase. Subunit III (P. denitrificans)
file_name:COX-para-III.txt
entry_date:6may1999
refman_number:7109,19016
endnote_number:
author:Iwata,S., Ostermeier,C., Ludwig,B., Michel,H. (1995) [Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans] {Nature, 376, 660-669}
remarks:Chain C in PDB file. Nterm in = cytoplasm. See also J. Biol. Chem. (1999), 274:33296-33299. Sequence from Swiss Prot. TMhelices=7.
pir_number:S03807
Swiss_Prot_entry:COX3_PARDE
Swiss_Prot_number:P06030
Swiss_Prot_gene:CTAE,COIII
Swiss_Prot_name:Cytochrome c oxidase polypeptide III
PDB_title:Cytochrome C Oxidase Polypeptide III
PDB_Identifier:1QLE
N_terminal:in
number_tmsegs:7
tm_segments:A.15,35;B.48,76;C.79,114;D.139,165;E.168,196;F.203,236;G.244,273
sequence:AHVKNHDYQILPPSIWPFFGAIGAFVMLTGAVAWMKGITFFGLPVEGPWMFLIGLVGVLYVMFGWWADVVNEGETGEHTPVVRIGLQYGFILFIMSEVMFFVAWFWAFIKNALYPMGPDSPIKDGVWPPEGIVTFDPWHLPLINTLILLLSGVAVTWAHHAFVLEGDRKTTINGLIVAVILGVCFTGLQAYEYSHAAFGLADTVYAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFLFVVIYIWGR*
>3D_helix;45
protein_name:cyto. C oxidase. Subunit IV (bovine)
file_name:COX-bov-IV.txt
entry_date:8jun98
refman_number:8424,7153
endnote_number:
author:Tsukihara,T., Aoyama,H., Yamashita,E., Tomizaki,T., Yamaguchi,H., Shinzawa-Itoh,K., Nakashima,R., Yaono,R., Yoshikawa,S. (1996) [The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å] {Science, 272, 1136-1144}
remarks:Chain D in PDB file. Nterm in = matrix. Sequence is processed sequence from Swiss-Prot (22 AA signal sequence removed). TMhelices=1.
pir_number:OLBO4
Swiss_Prot_entry:CX41_BOVIN
Swiss_Prot_number:P00423
Swiss_Prot_gene:COX4I1,COX4
Swiss_Prot_name:Cytochrome c oxidase subunit IV isoform 1, mitochondrial [Precursor]
PDB_title:cytochrome c oxidase
PDB_Identifier:1OCC
N_terminal:in
number_tmsegs:1
tm_segments:A.77,103
sequence:AHGSVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELYRLKFKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWKK*
>3D_helix;177
protein_name:cyto. C oxidase. Subunit IV (P. denitrificans)
file_name:COX-para-IV.txt
entry_date:2jan04
refman_number:7109,19016
endnote_number:
author:Iwata,S., Ostermeier,C., Ludwig,B., Michel,H. (1995) [Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans] {Nature, 376, 660-669}
remarks:Chain D in PDB file. See also J. Biol. Chem. (1999), 274:33296-33299. Sequence from Swiss Prot. TMhelices=1.
pir_number:S03807
Swiss_Prot_entry:COX4_PARDE
Swiss_Prot_number:P77921
Swiss_Prot_gene:CTAH
Swiss_Prot_name:Cytochrome c oxidase polypeptide IV
PDB_title:Cytochrome C Oxidase
PDB_Identifier:1QLE
N_terminal:in
number_tmsegs:1
tm_segments:A.17,48
sequence:ASHHEITDHKHGEMDIRHQQATFAGFIKGATWVSILSIAVLVFLALANS*
>3D_helix;46
protein_name:cyto. C oxidase. Subunit VIa (bovine)
file_name:COX-bov-VIa.txt
entry_date:8jun98
refman_number:8424,7153
endnote_number:
author:Tsukihara,T., Aoyama,H., Yamashita,E., Tomizaki,T., Yamaguchi,H., Shinzawa-Itoh,K., Nakashima,R., Yaono,R., Yoshikawa,S. (1996) [The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å] {Science, 272, 1136-1144}
remarks:Chain G in PDB file. Nterm in = matrix. Nterm buried within membrane. Nterm end of helix is 'in'. Sequence is processed sequence from Swiss-Prot (12 AA signal sequence removed). TMhelices=1.
pir_number:OGBO6
Swiss_Prot_entry:CX6A2_BOVIN
Swiss_Prot_number:P07471
Swiss_Prot_gene:COX6A2,COX6A
Swiss_Prot_name:Cytochrome c oxidase polypeptide VIa-heart, mitochondrial [Precursor]
PDB_title:cytochrome c oxidase
PDB_Identifier:1OCC
N_terminal:in
number_tmsegs:1
tm_segments:A.13,37
sequence:ASAAKGDHGGTGARTWRFLTFGLALPSVALCTLNSWLHSGHRERPAFIPYHHLRIRTKPFSWGDGNHTFFHNPRVNPLPTGYEKP*
>3D_helix;47
protein_name:cyto. C oxidase. Subunit VIc (bovine)
file_name:COX-bov-VIc.txt
entry_date:8jun98
refman_number:8424,7153
endnote_number:
author:Tsukihara,T., Aoyama,H., Yamashita,E., Tomizaki,T., Yamaguchi,H., Shinzawa-Itoh,K., Nakashima,R., Yaono,R., Yoshikawa,S. (1996) [The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å] {Science, 272, 1136-1144}
remarks:Chain I in PDB file. Nterm in = matrix. Sequence from Swiss-Prot. TMhelices=1.
pir_number:OGBO6C
Swiss_Prot_entry:COXH_BOVIN
Swiss_Prot_number:P04038
Swiss_Prot_gene:COX6C
Swiss_Prot_name:Cytochrome c oxidase polypeptide VIc
PDB_title:cytochrome c oxidase
PDB_Identifier:1OCC
N_terminal:in
number_tmsegs:1
tm_segments:A.12,52
sequence:STALAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDFEEMRKAGIFQSAK*
>3D_helix;48
protein_name:cyto. C oxidase. Subunit VIIa (bovine)
file_name:COX-bov-VIIa.txt
entry_date:8jun98
refman_number:8424,7153
endnote_number:
author:Tsukihara,T., Aoyama,H., Yamashita,E., Tomizaki,T., Yamaguchi,H., Shinzawa-Itoh,K., Nakashima,R., Yaono,R., Yoshikawa,S. (1996) [The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å] {Science, 272, 1136-1144}
remarks:Chain J in PDB file. Nterm in = matrix. Sequence is processed sequence from Swiss-Prot (21 AA signal sequence removed). TMhelices=1.
pir_number:OSBO7A
Swiss_Prot_entry:COXK_BOVIN
Swiss_Prot_number:P07470
Swiss_Prot_gene:COX7A1,COX7AH,COX7A
Swiss_Prot_name:Cytochrome c oxidase polypeptide VIIa-heart, mitochondrial [Precursor]
PDB_title:cytochrome c oxidase
PDB_Identifier:1OCC
N_terminal:in
number_tmsegs:1
tm_segments:A.26,54
sequence:FENRVAEKQKLFQEDNGLPVHLKGGATDNILYRVTMTLCLGGTLYSLYCLGWASFPHKK*
>3D_helix;50
protein_name:cyto. C oxidase. Subunit VIIc (bovine)
file_name:COX-bov-VIIc.txt
entry_date:8jun98
refman_number:8424,7153
endnote_number:
author:Tsukihara,T., Aoyama,H., Yamashita,E., Tomizaki,T., Yamaguchi,H., Shinzawa-Itoh,K., Nakashima,R., Yaono,R., Yoshikawa,S. (1996) [The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å] {Science, 272, 1136-1144}
remarks:Chain L in PDB file. Nterm in = matrix. Sequence is processed sequence from Swiss-Prot (16 AA signal sequence removed). TMhelices=1.
pir_number:OSBO8A
Swiss_Prot_entry:COX7C_BOVIN
Swiss_Prot_number:P00430
Swiss_Prot_gene:COX7C,COX7CP1
Swiss_Prot_name:Cytochrome c oxidase polypeptide VIIc, mitochondrial [Precursor]
PDB_title:cytochrome c oxidase
PDB_Identifier:1OCC
N_terminal:in
number_tmsegs:1
tm_segments:A.18,44
sequence:SHYEEGPGKNIPFSVENKWRLLAMMTLFFGSGFAAPFFIVRHQLLKK*
>3D_helix;51
protein_name:cyto. C oxidase. Subunit VIII (bovine)
file_name:COX-bov-VIII.txt
entry_date:8jun98
refman_number:8424,7153
endnote_number:
author:Tsukihara,T., Aoyama,H., Yamashita,E., Tomizaki,T., Yamaguchi,H., Shinzawa-Itoh,K., Nakashima,R., Yaono,R., Yoshikawa,S. (1996) [The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å] {Science, 272, 1136-1144}
remarks:Chain M in PDB file. Nterm in = matrix. Sequence is processed sequence from Swiss-Prot (24 AA signal sequence removed). TMhelices=1.
pir_number:OSBO8
Swiss_Prot_entry:COXQ_BOVIN
Swiss_Prot_number:P10175
Swiss_Prot_gene:COX8H
Swiss_Prot_name:Cytochrome c oxidase polypeptide VIII-heart, mitochondrial [Precursor]
PDB_title:cytochrome c oxidase
PDB_Identifier:1OCC
N_terminal:in
number_tmsegs:1
tm_segments:A.12,36
sequence:ITAKPARTPTSPKEQAIGLSVTFLSFLLPAGWVLYHLDNYKKSSAA*
>3D_helix;84
protein_name:cyto.c oxidase. Chain I (Thermus thermophilus)
file_name:COX-therm-I.txt
entry_date:11jul00
refman_number:18830,18879
endnote_number:
author:Soulimane, T., Buse, G., Bourenkov, G.P., Bartunik, H.D., Huber, R., and Than, M.E. (2000) [Structure and mechanism of the aberrant ba3-cytochrome c oxidase from Thermus thermophilus] {EMBO J., 19, 1766-1776}
remarks:Chain A in PDB file. Sequence from Swiss-Prot. cytoplasm = in. TMhelices=13.
pir_number:T52481
Swiss_Prot_entry:COX1_THETH
Swiss_Prot_number:Q56408
Swiss_Prot_gene:CBAA
Swiss_Prot_name:Cytochrome c oxidase polypeptide I
PDB_title:Ba3-Type Cytochrome-C Oxidase, chain A
PDB_Identifier:1EHK
N_terminal:in
number_tmsegs:13
tm_segments:A.17,48;B.65,97;C.103,125;D.143,173;E.181,212;F.221,254;G.262,283;H.292,326;I.344,366;J.380,409;K.415,444;L.461,493;M.527,550
sequence:MAVRASEISRVYEAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLLKRLLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGLMWLSWWMAFIGLVVAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLSTWVSIYIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAVLFLLPWSFGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLGFIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAEAPLPFAEVISGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNPVPGWRLW*
>3D_helix;85
protein_name:cyto.c oxidase. Chain II (Thermus thermophilus)
file_name:COX-therm-II.txt
entry_date:11jul00
refman_number:18830,18879
endnote_number:
author:Soulimane, T., Buse, G., Bourenkov, G.P., Bartunik, H.D., Huber, R., and Than, M.E. (2000) [Structure and mechanism of the aberrant ba3-cytochrome c oxidase from Thermus thermophilus] {EMBO J., 19, 1766-1776}
remarks:Chain B in PDB file. Sequence from Swiss-Prot. cytoplasm = in. TMhelices=1.
pir_number:T52480
Swiss_Prot_entry:COX2_THETH
Swiss_Prot_number:P98052
Swiss_Prot_gene:CBAB,CTAC
Swiss_Prot_name:Cytochrome c oxidase polypeptide II
PDB_title:Ba3-Type Cytochrome-C Oxidase, chain B
PDB_Identifier:1EHK
N_terminal:in
number_tmsegs:1
tm_segments:A.4,38
sequence:MVDEHKAHKAILAYEKGWLAFSLAMLFVFIALIAYTLATHTAGVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE*
>3D_helix;93
protein_name:cyto.c oxidase. Chain IIa (Thermus thermophilus)
file_name:COX-therm-IIa.txt
entry_date:27jan01
refman_number:19492
endnote_number:
author:Soulimane,T., Than,M.E., Dewor,M., Huber,R., and Buse,G. (2000) [Primary structure of a novel subunit in ba3-cytochrome c oxidase from Thermus thermophilus] {Protein Sci, 9, 2068-2073}
remarks:Chain C in PDB file. Sequence is from Swiss-Prot. cytoplasm = in. TMhelices=1.
pir_number:
Swiss_Prot_entry:COXA_THETH
Swiss_Prot_number:P82543
Swiss_Prot_gene:CBAD
Swiss_Prot_name:Cytochrome c oxidase polypeptide IIA
PDB_title:Ba3-Type Cytochrome-C Oxidase, chain C
PDB_Identifier:1EHK
N_terminal:in
number_tmsegs:1
tm_segments:A.4,34
sequence:MEEKPKGALAVILVLTLTILVFWLGVYAVFFARG*
>3D_helix;228
protein_name:F-type Na+-ATPase Subunit C (Ilyobacter tartaricus)
file_name:Na+-ATPase_Ilyo_tart.txt
entry_date:27jul05
refman_number:21818
endnote_number:
author:Meier,T., Polzer,P., Diederichs,K., Welte,W., Dimroth,P. (2005) [Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter tartaricus] {Science, 308, 659-662}
remarks:Homodimer. Sequence for monomer from Swiss-Prot. For context of this protein, see 1QO1 (ATP synthase rotary motor)
pir_number:
Swiss_Prot_entry:Q8KRV3_9FUSO
Swiss_Prot_number:Q8KRV3
Swiss_Prot_gene:atpE
Swiss_Prot_name:Subunit C
PDB_title:Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter tartaricus
PDB_Identifier:1YCE
N_terminal:out
number_tmsegs:2
tm_segments:A.4,44;B.48,80
sequence:MDMLFAKTVVLAASAVGAGTAMIAGIGPGVGQGYAAGKAVESVARQPEAKGDIISTMVLGAVAESTGIYSLVIALILLYANPFVGLLG*
>3D_helix;80
protein_name:F1F0 ATPsynthase Subunit C (E. coli)
file_name:ATPsynthase_C.txt
entry_date:12dec99
refman_number:16266,17900,17977
endnote_number:
author:Girvin,M.E., Rastogi,V.K., Abildgaard,F., Markley,J.L., Fillingame,R.H. (1998) [Solution structure of the transmembrane H+-transporting subunit c of the F1F0 ATP synthase] {Biochemistry, 37, 8817-8824}
remarks:Sequence is from Swiss-Prot. For context of this protein, see 1QO1 (ATP synthase rotary motor). TMhelices=2.
pir_number:LWECA
Swiss_Prot_entry:ATPL_ECOLI
Swiss_Prot_number:P00844
Swiss_Prot_gene:ATPE,UNCE,PAPH,B3737,C4665,Z5235,ECS4679,STM3870,STY3908,SF3817,YPO4126,Y4140
Swiss_Prot_name:ATP synthase C chain
PDB_title:F1F0 Atpase Subunit C
PDB_Identifier:1A91
N_terminal:out
number_tmsegs:2
tm_segments:A.2,39;B.47,77
sequence:MENLNMDLLYMAAAVMMGLAAIGAAIGIGILGGKFLEGAARQPDLIPLLRTQFFIVMGLVDAIPMIAVGLGLYVMFAVA*
>3D_helix;117
protein_name:formate dehydrogenase-N, beta chain (E. coli)
file_name:Fdn-N_beta.txt
entry_date:20oct02
refman_number:20602
endnote_number:
author:Jormakka,M., Törnroth,S., Byrne,B., Iwata,S. (2002) [Molecular basis of proton motive force generation: Structure of formate dehydrogenase-N] {Science, 295, 1863-1868}
remarks:Chain B in PDB. Sequence from Swiss-Prot. TMhelices=1.
pir_number:JS0629
Swiss_Prot_entry:FDNH_ECOLI
Swiss_Prot_number:P24184
Swiss_Prot_gene:FDNH,B1475,SF1750
Swiss_Prot_name:Formate dehydrogenase, nitrate-inducible, iron-sulfur subunit
PDB_title:formate dehydrogenase, nitrate-inducible, major subunit
PDB_Identifier:1KQF,1KQG
N_terminal:out
number_tmsegs:1
tm_segments:A.248,280
sequence:MAMETQDIIKRSATNSITPPSQVRDYKAEVAKLIDVSTCIGCKACQVACSEWNDIRDEVGHCVGVYDNPADLSAKSWTVMRFSETEQNGKLEWLIRKDGCMHCEDPGCLKACPSAGAIIQYANGIVDFQSENCIGCGYCIAGCPFNIPRLNKEDNRVYKCTLCVDRVSVGQEPACVKTCPTGAIHFGTKKEMLELAEQRVAKLKARGYEHAGVYNPEGVGGTHVMYVLHHADQPELYHGLPKDPKIDTSVSLWKGALKPLAAAGFIATFAGLIFHYIGIGPNKEVDDDEEDHHE*
>3D_helix;118
protein_name:formate dehydrogenase-N, gamma chain (E. coli)
file_name:Fdn-N_gamma.txt
entry_date:20oct02
refman_number:20602
endnote_number:
author:Jormakka,M., Törnroth,S., Byrne,B., Iwata,S. (2002) [Molecular basis of proton motive force generation: Structure of formate dehydrogenase-N] {Science, 295, 1863-1868}
remarks:Chain C in PDB. Sequence from Swiss-Prot. TMhelices=4.
pir_number:JS0630
Swiss_Prot_entry:FDNI_ECOLI
Swiss_Prot_number:P24185
Swiss_Prot_gene:FDNI,B1476,Z2234,ECS2080,SF1749
Swiss_Prot_name:Formate dehydrogenase, nitrate-inducible, cytochrome b556(FDN) subunit
PDB_title:formate dehydrogenase, nitrate-inducible, major subunit
PDB_Identifier:1KQG,1KQF
N_terminal:in
number_tmsegs:4
tm_segments:A.15,37;B.51,74;C.112,134;D.146,175
sequence:MSKSKMIVRTKFIDRACHWTVVICFFLVALSGISFFFPTLQWLTQTFGTPQMGRILHPFFGIAIFVALMFMFVRFVHHNIPDKKDIPWLLNIVEVLKGNEHKVADVGKYNAGQKMMFWSIMSMIFVLLVTGVIIWRPYFAQYFPMQVVRYSLLIHAAAGIILIHAILIHMYMAFWVKGSIKGMIEGKVSRRWAKKHHPRWYREIEKAEAKKESEEGI*
>3D_helix;79
protein_name:Fumarate Reductase alpha subunit (W. succinogenes)
file_name:Fum_Reduct_Wsuccin.txt
entry_date:14dec99
refman_number:17951
endnote_number:
author:Lancaster,C.R.D., Kröger, A., Auer,M., Michel,H. (1999) [Structure of fumarate reductase from Wolinella succinogenes at 2.2 Å resolution] {Nature, 402, 377-385}
remarks:Chain C in PDB file. Nterm in = cytoplasm. Sequence from Swiss-Prot. TMhelices=5.
pir_number:S10164
Swiss_Prot_entry:FRDC_WOLSU
Swiss_Prot_number:P17413
Swiss_Prot_gene:FRDC
Swiss_Prot_name:Fumarate reductase cytochrome B subunit
PDB_title:Fumarate Reductase Cytochrome B Subunit, Chain C, F. Other details - Haem Axial Ligands - His 44, His 93, His 143, His 182
PDB_Identifier:1QLA
N_terminal:in
number_tmsegs:5
tm_segments:A.22,52;B.77,100;C.121,149;D.169,194;E.202,237
sequence:MTNESILESYSGVTPERKKSRMPAKLDWWQSATGLFLGLFMIGHMFFVSTILLGDNVMLWVTKKFELDFIFEGGKPIVVSFLAAFVFAVFIAHAFLAMRKFPINYRQYLTFKTHKDLMRHGDTTLWWIQAMTGFAMFFLGSVHLYIMMTQPQTIGPVSSSFRMVSEWMWPLYLVLLFAVELHGSVGLYRLAVKWGWFDGETPDKTRANLKKLKTLMSAFLIVLGLLTFGAYVKKGLEQTDPNIDYKYFDYKRTHHR*
>3D_helix;75
protein_name:Fumarate Reductase. 13 kD anchor (E. coli)
file_name:Fum_Reduct_Ecoli_Ancr13.txt
entry_date:25aug99
refman_number:17670
endnote_number:
author:Iverson,T.M., Luna-Chavez,C., Cecchini,G., Rees,D.C. (1999) [Structure of the Escherichia coli fumarate reductase respiratory complex] {Science, 284, 1961-1966}
remarks:Chain D in PDB file. Helix A strongly (strangely!) kinked at about Ile26. Nterm in = cytoplasm. Sequence from Swiss-Prot. TMhelices=3.
pir_number:WMEC13
Swiss_Prot_entry:FRDD_ECOLI
Swiss_Prot_number:P03806
Swiss_Prot_gene:FRDD,B4151,Z5758,ECS5132,SF4309
Swiss_Prot_name:Fumarate reductase 13 kDa hydrophobic protein
PDB_title:Fumarate Reductase 13 Kda Hydrophobic Protein
PDB_Identifier:1L0V
N_terminal:in
number_tmsegs:3
tm_segments:A.9,35;B.61,89;C.97,115
sequence:MINPNPKRSDEPVFWGLFGAGGMWSAIIAPVMILLVGILLPLGLFPGDALSYERVLAFAQSFIGRVFLFLMIVLPLWCGLHRMHHAMHDLKIHVPAGKWVFYGLAAILTVVTLIGVVTI*
>3D_helix;74
protein_name:Fumarate Reductase. 15 kD anchor (E. coli)
file_name:Fum_Reduct_Ecoli_Ancr15.txt
entry_date:25aug99
refman_number:17670
endnote_number:
author:Iverson,T.M., Luna-Chavez,C., Cecchini,G., Rees,D.C. (1999) [Structure of the Escherichia coli fumarate reductase respiratory complex] {Science, 284, 1961-1966}
remarks:Chain C in PDB file. Helix A and B connected by very short turns to an interfacial helix (N51-L63). Nterm in = cytoplasm. Sequence from Swiss-Prot. TMhelices=3.
pir_number:S56380
Swiss_Prot_entry:FRDC_ECOLI
Swiss_Prot_number:P03805
Swiss_Prot_gene:FRDC,B4152,C5240,Z5759,ECS5133
Swiss_Prot_name:Fumarate reductase 15 kDa hydrophobic protein
PDB_title:fumarate reductase 15 kD hydrophobic protein, Chain C
PDB_Identifier:1FUM
N_terminal:in
number_tmsegs:3
tm_segments:A.22,49;B.66,90;C.105,128
sequence:MTTKRKPYVRPMTSTWWKKLPFYRFYMLREGTAVPAVWFSIELIFGLFALKNGPEAWAGFVDFLQNPVIVIINLITLAAALLHTKTWFELAPKAANIIVKDEKMGPEPIIKSLWAVTVVATIVILFVALYW*
>3D_helix;92
protein_name:Glycerol Channel, GlpF* (E. coli)
file_name:glycerol_channel.txt
entry_date:08nov00
refman_number:19203
endnote_number:
author:Fu,D., Libson,A., Miercke,L.J.W., Weitzman,C., Nollert,P., Krucinski,J., Stroud,R.M. (2000) [Structure of a glycerol-conducting channel and the basis for its selectivity] {Science, 290, 481-486}
remarks:One of the TM segments, C* + *C, is composed of two end-to-end helical segments. The two partial segments are counted as 2 TM segments topologically. Sequence from Swiss-Prot. TMhelices=6.
pir_number:XMECGF
Swiss_Prot_entry:GLPF_ECOLI
Swiss_Prot_number:P11244
Swiss_Prot_gene:GLPF,B3927,C4879,Z5472,ECS4852
Swiss_Prot_name:Glycerol uptake facilitator protein
PDB_title:Glycerol Uptake Facilitator Protein, Chain A
PDB_Identifier:1FX8
N_terminal:in
number_tmsegs:8
tm_segments:A.6,35;B.40,60;C*.68,77;D.85,108;E.144,169;F.178,194;*C.204,217;G.232,254
sequence:MSQTSTLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAGVSGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGSVESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLLIGLLIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAIVGAFAYRKLIGRHLPCDICVVEEKETTTPSEQKASL*
>3D_helix;138
protein_name:glycerol-3-phosphate transporter (E. coli)
file_name:GlpT.txt
entry_date:4dec03
refman_number:21092
endnote_number:
author:Huang,Y.F., Lemieux,M.J., Song,J.M., Auer,M., Wang,D.-N. (2003) [Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli] {Science, 301, 616-620}
remarks:sequence is from Swiss-Prot, which differs somewhat from PDB. Sequence numbering in PDB corresponds to Swiss-Prot sequence. TMhelices=12.
pir_number:JNECGT
Swiss_Prot_entry:GLPT_ECOLI
Swiss_Prot_number:P08194
Swiss_Prot_gene:Glycerol-3-phosphate transporter
Swiss_Prot_name:GLPT or B2240
PDB_title:Glycerol-3-phosphate transporter
PDB_Identifier:1PW4
N_terminal:in
number_tmsegs:12
tm_segments:A.20,57;B.64,88;C.94,112;D.121,147;E.153,180;F.190,207;G.253,282;H.288,316;I.322,341;J.347,374;K.380,409;L.415,448
sequence:MLSIFKPAPHKARLPAAEIDPTYRRLRWQIFLGIFFGYAAYYLVRKNFALAMPYLVEQGFSRGDLGFALSGISIAYGFSKFIMGSVSDRSNPRVFLPAGLILAAAVMLFMGFVPWATSSIAVMFVLLFLCGWFQGMGWPPCGRTMVHWWSQKERGGIVSVWNCAHNVGGGIPPLLFLLGMAWFNDWHAALYMPAFCAILVALFAFAMMRDTPQSCGLPPIEEYKNDYPDDYNEKAEQELTAKQIFMQYVLPNKLLWYIAIANVFVYLLRYGILDWSPTYLKEVKHFALDKSSWAYFLYEYAGIPGTLLCGWMSDKVFRGNRGATGVFFMTLVTIATIVYWMNPAGNPTVDMICMIVIGFLIYGPVMLIGLHALELAPKKAAGTAAGFTGLFGYLGGSVAASAIVGYTVDFFGWDGGFMVMIGGSILAVILLIVVMIGEKRRHEQLLQERNGG*
>3D_helix;78
protein_name:glycophorin A (human)
file_name:glycophorin.txt
entry_date:16nov99
refman_number:11728,5803
endnote_number:
author:Furthmayr,H., Galardy,R.E., Tomita,M., Marchesi,V.T. (1978) [The intramembranous segment of human erythrocyte glycophorin A] {Arch Biochem Biophys, 185, 21-29}
remarks:Sequence is processed sequence from Swiss-Prot (19 AA signal sequence removed). TMhelices=1.
pir_number:GFHUE
Swiss_Prot_entry:GLPA_HUMAN
Swiss_Prot_number:P02724
Swiss_Prot_gene:GYPA,GPA
Swiss_Prot_name:Glycophorin A [Precursor]
PDB_title:Glycophorin A, Chain A
PDB_Identifier:1AFO
N_terminal:out
number_tmsegs:1
tm_segments:A.73,95
sequence:SSTTGVAMHTSTSSSVTKSYISSQTNDTHKRDTYAATPRAHEVSEISVRTVYPPEEETGERVQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKKSPSDVKPLPSPDTDVPLSSVEIENPETSDQ*
>3D_helix;62
protein_name:halorhodopsin (H. salinarium)
file_name:HR.txt
entry_date:8June00
refman_number:18678,1665,6650
endnote_number:
author:Kolbe,M., Besir, H., Essen,L.-O., Oesterhelt, D. (2000) [Structure of the light-driven chloride pump halorhodopsin at 1.8 Å resolution] {Science, 288, 1390-1396}
remarks:Sequence below is unprocessed sequence from Swiss-Prot. AA numbering in PDB file and in the 'tmseg' assignments correspond to unprocessed sequence. Signal sequence corresponds to first 21 AA. TMhelices=7.
pir_number:A26161
Swiss_Prot_entry:BACH_HALSA
Swiss_Prot_number:P16102
Swiss_Prot_gene:HOP,VNG0180G
Swiss_Prot_name:Halorhodopsin [Precursor]
PDB_title:Halorhodopsin - Chain A
PDB_Identifier:1E12
N_terminal:out
number_tmsegs:7
tm_segments:A.26,51;B.58,81;C.106,127;D.131,154;E.158,180;F.193,216;G.227,255
sequence:MSITSVPGVVDAGVLGAQSAAAVRENALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFRWAFYAISCAFFVVVLSALVTDWAASASSAGTAEIFDTLRVLTVVLWLGYPIVWAVGVEGLALVQSVGVTSWAYSVLDVFAKYVFAFILLRWVANNERTVAVAGQTLGTMSSDD*
>3D_helix;56
protein_name:KcsA potassium channel* (S. lividans)
file_name:KcsA.txt
entry_date:25jun98
refman_number:15161
endnote_number:
author:Doyle,D.A., Cabral,J.M., Pfuetzner,R.A., Kuo,A., Gulbis,J.M., Cohen,S.L., Chait,B.T., MacKinnon,R. (1998) [The structure of the potassium channel: Molecular basis of K+ conduction and selectivity] {Science, 280, 69-77}
remarks:*The 'tmsegs' marked below include the so-called pore helix (P) associated with the pore region. 'tmseg' B corresponds to P. TMhelices=2.
pir_number:S60172
Swiss_Prot_entry:KCSA_STRCO
Swiss_Prot_number:Q54397
Swiss_Prot_gene:KCSA,SKC1,SCO7660,SC10F4.33
Swiss_Prot_name:Voltage-gated potassium channel
PDB_title:Potassium Channel (KcsA) from Streptomyces lividans
PDB_Identifier:1BL8
N_terminal:in
number_tmsegs:3
tm_segments:A.28,52;B.62,72;C.87,113
sequence:MPPMLSGLLARLVKLLLGRHGSALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQ*
>3D_helix;131
protein_name:KirBac1.1 potassium channel* (Burkholderia pseudomallei)
file_name:KirBac1.1.txt
entry_date:2july03
refman_number:21009
endnote_number:
author:Kuo,A., Gulbis,J.M., Antcliff,J.F., Rahman,T., Lowe,E.D., Zimmer,J., Cuthbertson,J., Ashcroft,F.M., Ezaki,T. Doyle,D.A. (2003) [Crystal structure of the potassium channel KirBac1.1 in the closed state] {Science, 300, 1922-1926}
remarks:*The 'tmsegs' marked below include the so-called pore-helix (P) associated with the pore region, and the so-called slide-helix (Sl). For 'tmsegs' below, A corresponds to Sl and C to P. Sequence is from TrEMBL. TMhelices=2.
pir_number:
Swiss_Prot_entry:P83698
Swiss_Prot_number:P83698
Swiss_Prot_gene:
Swiss_Prot_name:potassium channel
PDB_title:potassium channel
PDB_Identifier:1P7B
N_terminal:in
number_tmsegs:4
tm_segments:A.47,51;B.60,81;C.98,104;D.121,149
sequence:MNVDPFSPHSSDSFAQAASPARKPPRGGRRIWSGTREVIAYGMPASVWRDLYYWALKVSWPVFFASLAALFVVNNTLFALLYQLGDAPIANQSPPGFVGAFFFSVETLATVGYGDMHPQTVYAHAIATLEIFVGMSGIALSTGLVFARFARPRAKIMFARHAIVRPFNGRMTLMVRAANARQNVIAEARAKMRLMRREHSSEGYSLMKIHDLKLVRNEHPIFLLGWNMMHVIDESSPLFGETPESLAEGRAMLLVMIEGSDETTAQVMQARHAWEHDDIRWHHRYVDLMSDVDGMTHIDYTRFNDTEPVEPPGAAPDAQAFAAKPGEGDARPV*
>3D_helix;123
protein_name:KvAP potassium channel* (Aeropyrum pernix)
file_name:KvAP.txt
entry_date:13may03
refman_number:20977,20978,20979
endnote_number:
author:Jiang,Y.X., Lee,A., Chen,J.Y., Ruta,V., Cadene,M., Chait,B.T., MacKinnon,R.(2003) [X-ray structure of a voltage-dependent K+ channel] {Nature, 423, 33-41}
remarks:*The KvAP K-channel is complex. Of the 'tm segs' marked below, only tmsegs G and I are tmsegs in the usual sense. The others are associated with the pore helix and the voltage sensor domains. Using terminology from the Jiang et al. paper, the 'tmsegs' below have the following correspondence: A=S1, B=S2, C=S3a, D=S3b, E=S4, F=S4-S5 linker, G=S5, H=P, and I=S6.
pir_number:
Swiss_Prot_entry:below from TrEMBL
Swiss_Prot_number:Q9YDF8
Swiss_Prot_gene:APE0955
Swiss_Prot_name:295AA long hypothetical potassium channel
PDB_title:Voltage-Dependent Potassium Channel in complex with an Fab
PDB_Identifier:1ORQ
N_terminal:in
number_tmsegs:9
tm_segments:A.26,50;B.54,79;C.84,92;D.96,112;E.116,132;F.135,146;G.148,171;H.183,195;I.209,240
sequence:MARFRRGLSDLGGRVRNIGDVMEHPLVELGVSYAALLSVIVVVVEYTMQLSGEYLVRLYLVDLILVIILWADYAYRAYKSGDPAGYVKKTLYEIPALVPAGLLALIEGHLAGLGLFRLVRLLRFLRILLIISRGSKFLSAIADAADKIRFYHLFGAVMLTVLYGAFAIYIVEYPDPNSSIKSVFDALWWAVVTATTVGYGDVVPATPIGKVIGIAVMLTGISALTLLIGTVSNMFQKILVGEPEPSCSPAKLAEMVSSMSEEEFEEFVRTLKNLRRLENSMK*
>3D_helix;134
protein_name:lactose permease, 3D structure (E. coli)
file_name:LacPerm_3D.txt
entry_date:1dec03
refman_number:21091,19962,19600,17480,4992,16336
endnote_number:
author:Huang,Y.F., Lemieux,M.J., Song,J.M., Auer,M., Wang,D.-N.(2003) [Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli] {Science, 301, 610-615}
remarks:protein is a mutant:C154G. Sequence is thus from PDB file. TMhelices=12.
pir_number:GREC
Swiss_Prot_entry:LACY_ECOLI
Swiss_Prot_number:P02920
Swiss_Prot_gene:LACY,B0343
Swiss_Prot_name:Lactose permease
PDB_title:Lactose Permease
PDB_Identifier:1PV6,1PV7
N_terminal:in
number_tmsegs:12
tm_segments:A.6,34;B.42,70;C.75,100;D.104,136;E.140,164;F.166,186;G.221,247;H.254,276;I.288,304;J.312,340;K.343,376;L.378,399
sequence:MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALGASIVGIMFTINNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPGPLSLLRRQVNEVA*
>3D_helix;187
protein_name:LHC-II (Spinacia oleracea)
file_name:LHC_II-spinach.txt
entry_date:31mar04
refman_number:21404
endnote_number:
author:Liu,Z., Yan,H., Wang,K., Kuang,T., Zhang,J., Gui,L., An,X., Chang,W. (2004) [Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution] {Nature, 428, 287-292}
remarks:Sequence is from Swiss-Prot. The 35AA pre-sequence has been removed, consistent with PDB sequence. Stroma=in.
pir_number:JQ0020
Swiss_Prot_entry:CB21_SPIOL
Swiss_Prot_number:P12333
Swiss_Prot_gene:
Swiss_Prot_name:Chlorophyll a-b binding protein, chloroplast [Precursor]
PDB_title:Chlorophyll A-B Binding Protein, Chloroplast
PDB_Identifier:1RWT
N_terminal:in
number_tmsegs:3
tm_segments:A.55,86;B.124,144;C.170,201
sequence:RKTAGKPKTVQSSSPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWNFATNFVPGK*
>3D_helix;52
protein_name:Light Harvesting Complex. alpha chain (R. acidophila)
file_name:LHC-Racido-A.txt
entry_date:8jun98
refman_number:6653
endnote_number:
author:McDermott,G., Prince,S.M., Freer,A.A., Hawthornthwaite-Lawless,A.M., Papiz,M.Z., Cogdell,R.J., Issacs,N.W. (1995) [Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria] {Nature, 374, 517-521}
remarks:Chain A of PDB file. Sequence from Swiss-Prot. TMhelices=1.
pir_number:S06365
Swiss_Prot_entry:LHA4_RHOAC
Swiss_Prot_number:P26789
Swiss_Prot_gene:
Swiss_Prot_name:Light-harvesting protein B-800/850, alpha chain
PDB_title:integral membrane peripheral light harvesting complex from Rhodopseudomonas acidophila strain 10050
PDB_Identifier:1KZU
N_terminal:in
number_tmsegs:1
tm_segments:A.11,36
sequence:MNQGKIWTVVNPAIGIPALLGSVTVIAILVHLAILSHTTWFPAYWQGGVKKAA*
>3D_helix;54
protein_name:Light Harvesting Complex. alpha chain (R. molischianum)
file_name:LHC-Rmolis-A.txt
entry_date:8jun98
refman_number:8540
endnote_number:
author:Koepke,J., Hu,X., Muenke,C., Schulten,K., Michel,H. (1996) [The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum] {Structure, 4, 581-597}
remarks:Chain A of PDB file. Sequence from Swiss-Prot. TMhelices=1.
pir_number:A49290
Swiss_Prot_entry:LHA_RHOMO
Swiss_Prot_number:P97253
Swiss_Prot_gene:A1,A2,A3
Swiss_Prot_name:Light-harvesting protein B-800/850, alpha chain
PDB_title:crystal structure of the light-harvesting complex II 2 (B00-850) from Rhodospirillum molischianum
PDB_Identifier:1LGH
N_terminal:in
number_tmsegs:1
tm_segments:A.16,40
sequence:SNPKDDYKIWLVINPSTWLPVIWIVATVVAIAVHAAVLAAPGSNWIALGAAKSAAK*
>3D_helix;53
protein_name:Light Harvesting Complex. beta chain (R. acidophila)
file_name:LHC-Racido-B.txt
entry_date:8jun98
refman_number:6653
endnote_number:
author:McDermott,G., Prince,S.M., Freer,A.A., Hawthornthwaite-Lawless,A.M., Papiz,M.Z., Cogdell,R.J., Issacs,N.W. (1995) [Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria] {Nature, 374, 517-521}
remarks:Chain B of PDB file. Sequence from Swiss-Prot. TMhelices=1.
pir_number:S07673
Swiss_Prot_entry:LHB5_RHOAC
Swiss_Prot_number:P26790
Swiss_Prot_gene:
Swiss_Prot_name:Light-harvesting protein B-800/850, beta chain
PDB_title:integral membrane peripheral light harvesting complex from Rhodopseudomonas acidophila strain 10050
PDB_Identifier:1KZU
N_terminal:in
number_tmsegs:1
tm_segments:A.11,36
sequence:ATLTAEQSEELHKYVIDGTRVFLGLALVAHFLAFSATPWLH*
>3D_helix;55
protein_name:Light Harvesting Complex. beta chain (R. molischianum)
file_name:LHC-Rmolis-B.txt
entry_date:8jun98
refman_number:8540
endnote_number:
author:Koepke,J., Hu,X., Muenke,C., Schulten,K., Michel,H. (1996) [The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum] {Structure, 4, 581-597}
remarks:Chain B in PDB file. Sequence from Swiss-Prot. TMhelices=1.
pir_number:B49290
Swiss_Prot_entry:LHB1_RHOMO
Swiss_Prot_number:P95673
Swiss_Prot_gene:B1
Swiss_Prot_name:Light-harvesting protein B-800/850, beta 1 chain
PDB_title:crystal structure of the light-harvesting complex II 2 (B00-850) from Rhodospirillum molischianum
PDB_Identifier:1LGH
N_terminal:in
number_tmsegs:1
tm_segments:A.10,41
sequence:AERSLSGLTEEEAIAVHDQFKTTFSAFIILAAVAHVLVWVWKPWF*
>3D_helix;86
protein_name:M13 coat protein
file_name:m13.txt
entry_date:28jun01
refman_number:19804
endnote_number:
author:Bashtovy,D. Marsh,D., Hemminga,M.A., Páli,T. (2001) [Constrained modeling of spin-labeled major coat protein mutants from M13 bacteriophage in a phospholipid bilayer] {Protein Sci, 10, 979-987}
remarks:S-P differs from PDB sequence at two residue positions. Sequence from PDB. TMhelices=1.
pir_number:
Swiss_Prot_entry:COAB_BPZJ2
Swiss_Prot_number:P03618
Swiss_Prot_gene:VIII
Swiss_Prot_name:Coat protein B
PDB_title:M13 major coat protein
PDB_Identifier:2CPB,2CPS
N_terminal:out
number_tmsegs:1
tm_segments:A.24,45
sequence:AEGDDPAKAAFNSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS*
>3D_helix;259
protein_name:Metalloenzyme pMMO subunit pmoA (Methylococcus capsulatus)
file_name:Metalloenzyme_pMMO_subunit_pmoA_Methyl_capsul.txt
entry_date:07feb07
refman_number:
endnote_number:22072
author:Lieberman, R.L., Rosenzweig, A.C. (2005) [Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane] {Nature, 434, 177-182}
remarks:Homotrimer. Sequence for monomer from Swiss-Prot. This corresponds to chain B in PDB file. 2 TM segments, F and G are not a full TM helices. TM segment F is probably not a helix and TM segment G is only a partial helix.
pir_number:
Swiss_Prot_entry:Q607G3_METCA
Swiss_Prot_number:Q607G3
Swiss_Prot_gene:pmoA
Swiss_Prot_name:Methane monooxygenase, A subunit
PDB_title:Crystal structure of particulate methane monooxygenase
PDB_Identifier:1YEW
N_terminal:in
number_tmsegs:7
tm_segments:A.11,43;B.59,79;C.88,105;D.125,136;E.141,167;F.193,216;G.220,242
sequence:MSAAQSAVRSHAEAVQVSRTIDWMALFVVFFVIVGSYHIHAMLTMGDWDFWSDWKDRRLWVTVTPIVLVTFPAAVQSYLWERYRLPWGATVCVLGLLLGEWINRYFNFWGWTYFPINFVFPASLVPGAIILDTVLMLSGSYLFTAIVGAMGWGLIFYPGNWPIIAPLHVPVEYNGMLMSIADIQGYNYVRTGTPEYIRMVEKGTLRTFGKDVAPVSAFFSAFMSILIYFMWHFIGRWFSNERFLQST*
>3D_helix;260
protein_name:Metalloenzyme pMMO subunit pmoB (Methylococcus capsulatus)
file_name:Metalloenzyme_pMMO_subunit pmoB_Methyl_capsul.txt
entry_date:07feb07
refman_number:
endnote_number:22072
author:Lieberman, R.L., Rosenzweig, A.C. (2005) [Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane] {Nature, 434, 177-182}
remarks:Homotrimer. Sequence for monomer from Swiss-Prot. This corresponds to chain A in PDB file.
pir_number:B57266
Swiss_Prot_entry:Q49104_METCA
Swiss_Prot_number:Q49104
Swiss_Prot_gene:pmoB
Swiss_Prot_name:Particulate methane monooxygenase 45 kDa subunit [Precursor]
PDB_title:Crystal structure of particulate methane monooxygenase
PDB_Identifier:1YEW
N_terminal:out
number_tmsegs:2
tm_segments:A.185,207;B.232,256
sequence:MKTIKDRIAKWSAIGLLSAVAATAFYAPSASAHGEKSQAAFMRMRTIHWYDLSWSKEKVKINETVEIKGKFHVFEGWPETVDEPDVAFLNVGMPGPVFIRKESYIGGQLVPRSVRLEIGKTYDFRVVLKARRPGDWHVHTMMNVQGGGPIIGPGKWITVEGSMSEFRNPVTTLTGQTVDLENYNEGNTYFWHAFWFAIGVAWIGYWSRRPIFIPRLLMVDAGRADELVSATDRKVAMGFLAATILIVVMAMSSANSKYPITIPLQAGTMRGMKPLELPAPTVSVKVEDATYRVPGRAMRMKLTITNHGNSPIRLGEFYTASVRFLDSDVYKDTTGYPEDLLAEDGLSVSDNSPLAPGETRTVDVTASDAAWEVYRLSDIIYDPDSRFAGLLFFFDATGNRQVVQIDAPLIPSFM*
>3D_helix;261
protein_name:Metalloenzyme pMMO subunit pmoC (Methylococcus capsulatus)
file_name:Metalloenzyme_pMMO_subunit pmoC_Methyl_capsul.txt
entry_date:07feb07
refman_number:
endnote_number:22072
author:Lieberman, R.L., Rosenzweig, A.C. (2005) [Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane] {Nature, 434, 177-182}
remarks:Homotrimer. Sequence for monomer from Swiss-Prot. This corresponds to chain C in PDB file.
pir_number:
Swiss_Prot_entry:O05111_METCA
Swiss_Prot_number:O05111
Swiss_Prot_gene:pmoC2
Swiss_Prot_name:Methane monooxygenase subunit C2
PDB_title:Crystal structure of particulate methane monooxygenase
PDB_Identifier:1YEW
N_terminal:in
number_tmsegs:5
tm_segments:A.51,76;B.90,113;C.126,149;D.171,198;E.202,249
sequence:MHETKQGGEKRFTGAICRCSHRYNSMEVKMAATTIGGAAAAEAPLLDKKWLTFALAIYTVFYLWVRWYEGVYGWSAGLDSFAPEFETYWMNFLYTEIVLEIVTASILWGYLWKTRDRNLAALTPREELRRNFTHLVWLVAYAWAIYWGASYFTEQDGTWHQTIVRDTDFTPSHIIEFYLSYPIYIITGFAAFIYAKTRLPFFAKGISLPYLVLVVGPFMILPNVGLNEWGHTFWFMEELFVAPLHYGFVIFGWLALAVMGTLTQTFYSFAQGGLGQSLCEAVDEGLIAK*
>3D_helix;224
protein_name:Mito. Respiratory Complex protein CybL (pig)
file_name:Mito_respir_complex_CybL_pig.txt
entry_date:26jul05
refman_number:21880
endnote_number:
author:Sun,F., Huo,X., Zhai,Y., Wang,A., Xu,J., Su,D., Bartlam,M., Rao,Z. (2005) [Crystal structure of mitochondrial respiratory membrane protein complex II] {Cell, 121, 1043-1057}
remarks:Sequence from PDB,chain C. PDB sequence starts from res#4. Assigned TM segments account for this. TM helices correspond to 2L,4L and 5L in the article. No Swiss-Prot file for this protein. Matrix=in.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Crystal Structure of Mitochondrial Respiratory Complex II from porcine heart at 2.4 Angstroms
PDB_Identifier:1ZOY
N_terminal:in
number_tmsegs:3
tm_segments:A.34,62;B.81,109;C.116,137
sequence:LGTTAKEEMERFWNKNLGSNRPLSPHITIYRWSLPMAMSICHRGTGIALSAGVSLFGLSALLLPGNFESHLELVKSLCLGPTLIYTAKFGIVFPLMYHTWNGIRHLIWDLGKGLTIPQLTQSGVVVLILTVLSSVGLAAM*
>3D_helix;225
protein_name:Mito. Respiratory protein CybS (pig)
file_name:Mito_respir_complex_CybS_pig.txt
entry_date:26jul05
refman_number:21880
endnote_number:
author:Sun,F., Huo,X., Zhai,Y., Wang,A., Xu,J., Su,D., Bartlam,M., Rao,Z. (2005) [Crystal structure of mitochondrial respiratory membrane protein complex II] {Cell, 121, 1043-1057}
remarks:Sequence from PDB, chain D. PDB sequence starts with res#34. Assigned TM segments account for this. TM helices correspond to 1S,2S and 3S in the article. No Swiss-Prot file for this protein. Matrix=in.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Crystal Structure of Mitochondrial Respiratory Complex II from porcine heart at 2.4 Angstroms
PDB_Identifier:1ZOY
N_terminal:in
number_tmsegs:3
tm_segments:A.4,29;B.34,58;C.65,88
sequence:ASSKAASLHWTGERVVSVLLLGLLPAAYLNPCSAMDYSLAAALTLHGHWGIGQVVTDYVRGDALQKAAKAGLLALSAFTFAGLCYFNYHDVGICKAVAMLWKL*
>3D_helix;69
protein_name:MscL mechanosensor channel monomer (M. tuberculosis)
file_name:MscL.txt
entry_date:23apr99
refman_number:16898
endnote_number:
author:Chang,G., Spencer,R.H., Lee,A.T., Barclay,M.T., Rees,D.C. (1998) [Structure of the MscL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel] {Science, 282, 2220-2226}
remarks:Biological unit is a pentamer. Sequence from Swiss-Prot. TMhelices=2.
pir_number:E70821
Swiss_Prot_entry:MSCL_MYCTU
Swiss_Prot_number:O53898
Swiss_Prot_gene:Large-conductance mechanosensitive channel
Swiss_Prot_name:MSCL,RV0985C,MT1013,MTV044.13C
PDB_title:mechanosensitive ion channel
PDB_Identifier:1MSL
N_terminal:in
number_tmsegs:2
tm_segments:A.15,39;B.71,89
sequence:MLKGFKEFLARGNIVDLAVAVVIGTAFTALVTKFTDSIITPLINRIGVNAQSDVGILRIGIGGGQTIDLNVLLSAAINFFLIAFAVYFLVVLPYNTLRKKGEVEQPGDTQVVLLTEIRDLLAQTNGDSPGRHGGRGTPSPTDGPRASTESQ*
>3D_helix;119
protein_name:MscS mechanosensor channel monomer (E. coli)
file_name:MscS.txt
entry_date:26nov02
refman_number:20684
endnote_number:
author:Bass,R.B., Strop,P., Barclay,M., Rees,D.C. (2002) [Crystal structure of Escherichia coli McsS, a voltage-modulated and mechanosensitive channel] {Science, 298, 1582-1587}
remarks:Biological unit is a heptamer. Sequence from Swiss-Prot. PDB sequence is truncated relative to Swiss-Prot. TMhelices=3.
pir_number:QQEC4
Swiss_Prot_entry:MSCS_ECOLI
Swiss_Prot_number:P0C0S1
Swiss_Prot_gene:mscS,B2924
Swiss_Prot_name:small-conductance mechanosensitive channel
PDB_title:mechanosensitive channel protein
PDB_Identifier:1MXM
N_terminal:out
number_tmsegs:3
tm_segments:A.29,57;B.68,91;C.96,127
sequence:MEDLNVVDSINGAGSWLVANQALLLSYAVNIVAALAIIIVGLIIARMISNAVNRLMISRKIDATVADFLSALVRYGIIAFTLIAALGRVGVQTASVIAVLGAAGLAVGLALQGSLSNLAAGVLLVMFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSREPVRRNEFIIGVAYDSDIDQVKQILTNIIQSEDRILKDREMTVRLNELGASSINFVVRVWSNSGDLQNVYWDVLERIKREFDAAGISFPYPQMDVNFKRVKEDKAA*
>3D_helix;122
protein_name:MthK K+ channel* (Methanobacterium thermoautotrophicum)
file_name:MthK.txt
entry_date:17July02
refman_number:20342
endnote_number:
author:Jiang,Y.X., Lee,A., Chen,J.Y., Cadene,M., Chait,B.T., MacKinnon,R. (2002) [Crystal structure and mechanism of a calcium-gated potassium channel] {Nature, 417, 515-522}
remarks:*The 'tmsegs' marked below include the so-called pore-helix (P) associated with the pore region. 'tmseg' B corresponds to P. Sequence from Swiss-Prot. TMhelices=2.
pir_number:H69069
Swiss_Prot_entry:MTHK_METTH
Swiss_Prot_number:O27564
Swiss_Prot_gene:MTHK,MTH1520
Swiss_Prot_name:Calcium-gated potassium channel MthK
PDB_title:Potassium channel related protein
PDB_Identifier:1LNQ
N_terminal:in
number_tmsegs:3
tm_segments:A.19,40;B.49,57;C.72,95
sequence:MVLVIEIIRKHLPRVLKVPATRILLLVLAVIIYGTAGFHFIEGESWTVSLYWTFVTIATVGYGDSPSTPLGMYFTVTLIVLGIGTFAVAVERLLEFLINREQMKLMGLIDVAKSRHVVICGWSESTLECLRELRGSEVFVLAEDENVRKKVLRSGANFVHGDPTRVSDLEKANVRGARAVIVDLESDSETIHCILGIRKIDESVRIIAEAERYENIEQLRMAGADQVISPFVISGRLMSRSIDDGYEAMFVQDVLAEESTRRMVEVPIPEGSKLEGVSVLDADIHDVTGVIIIGVGRGDELIIDPPRDYSFRAGDIILGIGKPEEIERLKNYISA*
>3D_helix;233
protein_name:multidrug resistance protein EmrD (E.coli)
file_name:EmrD_Ecoli.txt
entry_date:23jul06
refman_number:
endnote_number:22063
author:Yin,Y., He,X., Szewczyk,P., Nguyen,T., Chang,G. (2006) [Structure of the multidrug transporter EmrD from Escherichia coli] {Science, 312, 741-744}
remarks:Sequence from Swiss-Prot
pir_number:
Swiss_Prot_entry:EMRD_ECOLI
Swiss_Prot_number:P31442
Swiss_Prot_gene:emrD
Swiss_Prot_name:Multidrug resistance protein D
PDB_title:Structure of the Multidrug Transporter EmrD from Escherichia coli
PDB_Identifier:2GFP
N_terminal:in
number_tmsegs:12
tm_segments:A.9,35;B.43,68;C.72,91;D.99,125;E.133,155;F.161,178;G.203,230;H.236,261;I.267,285;J.290,312;K.320,349;L.356,378
sequence:MKRQRNVNLLLMLVLLVAVGQMAQTIYIPAIADMARDLNVREGAVQSVMGAYLLTYGVSQLFYGPISDRVGRRPVILVGMSIFMLATLVAVTTSSLTVLIAASAMQGMGTGVGGVMARTLPRDLYERTQLRHANSLLNMGILVSPLLAPLIGGLLDTMWNWRACYLFLLVLCAGVTFSMARWMPETRPVDAPRTRLLTSYKTLFGNSGFNCYLLMLIGGLAGIAAFEACSGVLMGAVLGLSSMTVSILFILPIPAAFFGAWFAGRPNKRFSTLMWQSVICCLLAGLLMWIPDWFGVMNVWTLLVPAALFFFGAGMLFPLATSGAMEPFPFLAGTAGALVGGLQNIGSGVLASLSAMLPQTGQGSLGLLMTLMGLLIVLCWLPLATRMSHQGQPV*
>3D_helix;226
protein_name:Na+_H+_antiporter (E. coli)
file_name:Na+_H+_antiporter_Ecoli.txt
entry_date:26jul05
refman_number:21873
endnote_number:
author:Hunte,C., Screpanti,E., Venturi,M., Rimon,A., Padan,E., Michel,H. (2005) [Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH] {Nature, 435, 1197-1202}
remarks:Sequence from PDB. TM segment D and K consists two short alpha-Helices
pir_number:C64722
Swiss_Prot_entry:NHAA_ECOLI
Swiss_Prot_number:P13738
Swiss_Prot_gene:nhaA
Swiss_Prot_name:Na(+)/H(+) antiporter 1
PDB_title:Crystal structure of the Na+/H+ antiporter NhaA
PDB_Identifier:1ZCD
N_terminal:in
number_tmsegs:12
tm_segments:A.12,30;B.59,85;C.95,116;D.121,143;E.150,175;F.182,200;G.205,218;H.223,236;I.247,271;J.290,311;K.327,350;L.357,382
sequence:MKHLHRFFSSDASGGIILIIAAILAMIMANSGATSGWYHDFLETPVQLRVGSLEINKNMLLWINDALMAVFFLLVGLEVKRELMQGSLASLRQAAFPVIAAIGGMIVPALLYLAFNYADPITREGWAIPAATDIAFALGVLALLGSRVPLALKIFLMALAIIDDLGAIIIIALFYTNDLSMASLGVAAVAIAVLAVLNLCGARRTGVYILVGVVLWTAVLKSGVHATLAGVIVGFFIPLKEKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSLQGVTLDGLTSILPLGIIAGLLIGKPLGISLFCWLALRLKLAHLPEGTTYQQIMVVGILCGIGFTMSIFIASLAFGSVDPELINWAKLGILVGSISSAVIGYSWLRVRLRPSV*
>3D_helix;249
protein_name:NaK channel, Na+ complex (Bacillus cereus)
file_name:NaK_channel_Na+_Bcereus.txt
entry_date:29jan07
refman_number:
endnote_number:21983
author:Shi,N., Ye,S., Alam,A., Chen,L., Jiang,Y.(2006) [Atomic structure of a Na+- and K+-conducting channel] {Nature, 440, 570-574}
remarks:Tetrameric form. Sequence for monomer from Swiss_Prot.
pir_number:
Swiss_Prot_entry:Q81HW2_BACCR
Swiss_Prot_number:Q81HW2
Swiss_Prot_gene:BC_0669
Swiss_Prot_name:Potassium channel protein
PDB_title:Na+ complex of the NaK Channel
PDB_Identifier:2AHY
N_terminal:in
number_tmsegs:2
tm_segments:A.22,44;B.74,102
sequence:MLSFLLTLKRMLRACLRAWKDKEFQVLFVLTILTLISGTIFYSTVEGLRPIDALYFSVVTLTTVGDGNFSPQTDFGKIFTILYIFIGIGLVFGFIHKLAVNVQLPSILSNRKKE*
>3D_helix;163
protein_name:nitrate reductase A, NarI membrane anchor (E. coli)
file_name:NarI.txt
entry_date:23dec03
refman_number:21146
endnote_number:
author:Bertero,M.G., Rothery,R.A., Palak,M., Hou,C., Lim,D., Blasco,F., Weiner,J.H., Strynadka,N.C.J. (2003) [Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A] {Nature Struct Biol, 10, 681-687}
remarks:Sequence from Swiss-Prot. TMhelices=5.
pir_number:C27737, RDECNG
Swiss_Prot_entry:NARI_ECOLI
Swiss_Prot_number:P11350
Swiss_Prot_gene:NARI,CHLI,B1227
Swiss_Prot_name:Respiratory nitrate reductase 1 gamma chain
PDB_title:Respiratory Nitrate Reductase 1 gamma Chain
PDB_Identifier:1Q16
N_terminal:out
number_tmsegs:5
tm_segments:A.2,28;B.49,72;C.82,119;D.122,149;E.182,200
sequence:MQFLNMFFFDIYPYIAGAVFLIGSWLRYDYGQYTWRAASSQMLDRKGMNLASNLFHIGILGIFVGHFFGMLTPHWMYEAWLPIEVKQKMAMFAGGASGVLCLIGGVLLLKRRLFSPRVRATTTGADILILSLLVIQCALGLLTIPFSAQHMDGSEMMKLVGWAQSVVTFHGGASQHLDGVAFIFRLHLVLGMTLFLLFPFSRLIHIWSVPVEYLTRKYQLVRARH*
>3D_helix;235
protein_name:NrfH (Desulfovibrio vulgaris)
file_name:NfrH_Desul_vulgaris.txt
entry_date:18dec06
refman_number:
endnote_number:22330
author:Rodrigues,M.L., Oliveira,T.F., Pereira,I.A.C., Archer,M. (2006) [X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination] {EMBO J, 25, 5951-5960}
remarks:Sequence from PDB, chain C.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:CRYSTAL STRUCTURE OF CYTOCHROME C NITRITE REDUCTASE NRFHA COMPLEX FROM DESULFOVIBRIO VULGARIS
PDB_Identifier:2J7A
N_terminal:in
number_tmsegs:1
tm_segments:A.14,38
sequence:MSEEKSRNGPARLKLVLGGATLGVVALATVAFGMKYTDQRPFCTSCHIMNPVGVTHKLSGHANISCNDCHAPHNLLAKLPFKAIAGARDVYMNTLGHPGDLILAGMETKEVVNANCKACHTMTNVEVASMEAKKYCTDCHRNVQHMRMKPISTREVADE*
>3D_helix;232
protein_name:phospholamban pentamer (human)
file_name:phospholamban_human.txt
entry_date:11jul06
refman_number:
endnote_number:21386
author:Oxenoid,K., Chou,J.J. (2005) [The structure of phospholamban pentamer reveals a channel-like architecture in membranes] {Proc Natl Acad Sci USA, 102, 10870-10875}
remarks:Sequence from PDB. Sequence is for one monomer in pentamer. Also see 1FJK, 1FJP (cardiac phospholamban from pig)
pir_number:A40424
Swiss_Prot_entry:P26678
Swiss_Prot_number:PPLA_HUMAN
Swiss_Prot_gene:PLN
Swiss_Prot_name:Cardiac phospholamban
PDB_title:NMR Structure of Unphosphorylated Human Phospholamban Pentamer
PDB_Identifier:1ZLL
N_terminal:in
number_tmsegs:1
tm_segments:A.23,52
sequence:MEKVQYLTRSAIRRASTIEMPQQARQKLQNLFINFCLILICLLLICIIVMLL*
>3D_helix;98
protein_name:photosystem I A subunit (Synechococcus elongatus)
file_name:PS_I_PsaA.txt
entry_date:6jul01
refman_number:19835,16396,19598,16394,13836,20928
endnote_number:
author:Jordan,P., Fromme,P., Witt,H.T., Klukas,O., Saenger,W., Krauss,N. (2001) [Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution] {Nature, 411, 909-917}
remarks:Stroma=in. Sequence from Swiss-Prot. TMhelices=11.
pir_number:
Swiss_Prot_entry:PSAA_SYNEL
Swiss_Prot_number:P25896
Swiss_Prot_gene:PSAA,TLR0731
Swiss_Prot_name:Photosystem I P700 chlorophyll A apoprotein A1
PDB_title:PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1
PDB_Identifier:1JB0
N_terminal:in
number_tmsegs:11
tm_segments:A.65,97;B.155,181;C.193,227;D.294,311;E.352,376;F.387,418;G.437,468;H.533,558;I.591,620;J.670,691;K.724,755
sequence:MTISPPEREPKVRVVVDNDPVPTSFEKWAKPGHFDRTLARGPQTTTWIWNLHALAHDFDTHTSDLEDISRKIFSAHFGHLAVVFIWLSGMYFHGAKFSNYEAWLADPTGIKPSAQVVWPIVGQGILNGDVGGGFHGIQITSGLFQLWRASGITNEFQLYCTAIGGLVMAGLMLFAGWFHYHKRAPKLEWFQNVESMLNHHLAGLLGLGSLAWAGHQIHVSLPINKLLDAGVAAKDIPLPHEFILNPSLMAELYPKVDWGFFSGVIPFFTFNWAAYSDFLTFNGGLNPVTGGLWLSDTAHHHLAIAVLFIIAGHMYRTNWGIGHSLKEILEAHKGPFTGAGHKGLYEVLTTSWHAQLAINLAMMGSLSIIVAQHMYAMPPYPYLATDYPTQLSLFTHHMWIGGFLVVGGAAHGAIFMVRDYDPAMNQNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYVHNDTMRAFGRPQDMFSDTGIQLQPVFAQWVQNLHTLAPGGTAPNAAATASVAFGGDVVAVGGKVAMMPIVLGTADFMVHHIHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLFWMYNCISVVIFHFSWKMQSDVWGTVAPDGTVSHITGGNFAQSAITINGWLRDFLWAQASQVIGSYGSALSAYGLLFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPRALSIIQGRAVGVAHYLLGGIATTWAFFLARIISVG*
>3D_helix;99
protein_name:photosystem I B subunit (Synechococcus elongatus)
file_name:PS_I_PsaB.txt
entry_date:6jul01
refman_number:19835,16396,19598,16394,13836,20928
endnote_number:
author:Jordan,P., Fromme,P., Witt,H.T., Klukas,O., Saenger,W., Krauss,N. (2001) [Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution] {Nature, 411, 909-917}
remarks:Stroma=in. Sequence from Swiss-Prot. TMhelices=11.
pir_number:
Swiss_Prot_entry:PSAB_SYNEL
Swiss_Prot_number:P25897
Swiss_Prot_gene:PSAB,TLR0732
Swiss_Prot_name:Photosystem I P700 chlorophyll A apoprotein A2
PDB_title:PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2
PDB_Identifier:1JB0
N_terminal:in
number_tmsegs:11
tm_segments:A.38,70;B.131,154;C.170,201;D.269,286;E.333,357;F.368,399;G.418,448;H.520,545;I.578,609;J.650,671;K.707,738
sequence:ATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLWVSGSLFHVAWQGNFEQWVQDPVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGVYHWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPKFRPSLSWFKNAESRLNHHLAGLFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTASHVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHSIKEMMDAKDFFGTKVEGPFNMPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLPPYAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVRDYDPAQNKGNVLDRVLQHKEAIISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDTLLSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDKKDFGYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFYWHWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGTNNLSVWAWMFLFGHLVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHFSVGYILTYAAFLIASTAAKFG*
>3D_helix;100
protein_name:photosystem I F subunit* (Synechococcus elongatus)
file_name:PS_I_PsaF.txt
entry_date:6jul01
refman_number:19835,16396,19598,16394,13836,20928
endnote_number:
author:Jordan,P., Fromme,P., Witt,H.T., Klukas,O., Saenger,W., Krauss,N. (2001) [Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution] {Nature, 411, 909-917}
remarks:*Only helix A is transmembrane. Helix B does not cross the membrane, but is buried in it with a kink so that it enters and leaves from the same side (stromal) of the membrane. Stroma = in. Sequence is the processed sequence from Swiss-Prot (23 AA signal sequence removed).
pir_number:
Swiss_Prot_entry:PSAF_SYNEL
Swiss_Prot_number:P0A401
Swiss_Prot_gene:PSAF,TLR2411
Swiss_Prot_name:Photosystem I reaction centre subunit III [Precursor]
PDB_title:PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III
PDB_Identifier:1JB0
N_terminal:out
number_tmsegs:2
tm_segments:A.64,89;B.104,126
sequence:DVAGLVPCKDSPAFQKRAAAAVNTTADPASGQKRFERYSQALCGEDGLPHLVVDGRLSRAGDFLIPSVLFLYIAGWIGWVGRAYLIAVRNSGEANEKEIIIDVPLAIKCMLTGFAWPLAALKELASGELTAKDNEITVSPR*
>3D_helix;101
protein_name:photosystem I I subunit(Synechococcus elongatus)
file_name:PS_I_PsaI.txt
entry_date:6jul01
refman_number:19835,16396,19598,16394,13836,20928
endnote_number:
author:Jordan,P., Fromme,P., Witt,H.T., Klukas,O., Saenger,W., Krauss,N. (2001) [Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution] {Nature, 411, 909-917}
remarks:Stroma=in. Sequence from Swiss-Prot. TMhelices=1.
pir_number:
Swiss_Prot_entry:PSAI_SYNEL
Swiss_Prot_number:P25900
Swiss_Prot_gene:PSAI,TSR2405
Swiss_Prot_name:Photosystem I reaction center subunit VIII
PDB_title:PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII
PDB_Identifier:1JB0
N_terminal:out
number_tmsegs:1
tm_segments:A.10,35
sequence:MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA*
>3D_helix;102
protein_name:photosystem I J subunit (Synechococcus elongatus)
file_name:PS_I_PsaJ.txt
entry_date:6jul01
refman_number:19835,16396,19598,16394,13836,20928
endnote_number:
author:Jordan,P., Fromme,P., Witt,H.T., Klukas,O., Saenger,W., Krauss,N. (2001) [Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution] {Nature, 411, 909-917}
remarks:Stroma=in. Sequence from Swiss-Prot. TMhelices=1.
pir_number:
Swiss_Prot_entry:PSAJ_SYNEL
Swiss_Prot_number:P25901
Swiss_Prot_gene:PSAJ,TSR2412
Swiss_Prot_name:Photosystem I reaction center subunit IX
PDB_title:PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX
PDB_Identifier:1JB0
N_terminal:out
number_tmsegs:1
tm_segments:A.11,31
sequence:MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL*
>3D_helix;103
protein_name:photosystem I K subunit (Synechococcus elongatus)
file_name:PS_I_PsaK.txt
entry_date:6jul01
refman_number:19835,16396,19598,16394,13836,20928
endnote_number:
author:Jordan,P., Fromme,P., Witt,H.T., Klukas,O., Saenger,W., Krauss,N. (2001) [Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution] {Nature, 411, 909-917}
remarks:Stroma=in. Sequence is unprocessed sequence from Swiss-Prot, which corresponds to AA numbering in PDB file. TMhelices=2.
pir_number:
Swiss_Prot_entry:PSAK_SYNEL
Swiss_Prot_number:P20453
Swiss_Prot_gene:PSAK,TSR2273
Swiss_Prot_name:Photosystem I reaction center subunit psaK [Precursor]
PDB_title:PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X
PDB_Identifier:1JB0
N_terminal:out
number_tmsegs:2
tm_segments:A.20,36;B.55,77
sequence:MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELLATTSFGHLLAAGVVSGLQYAGAL*
>3D_helix;104
protein_name:photosystem I L subunit (Synechococcus elongatus)
file_name:PS_I_PsaL.txt
entry_date:6jul01
refman_number:19835,16396,19598,16394,13836,20928
endnote_number:
author:Jordan,P., Fromme,P., Witt,H.T., Klukas,O., Saenger,W., Krauss,N. (2001) [Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution] {Nature, 411, 909-917}
remarks:Stroma = in. Sequence is from Swiss-Prot, with Met1 removed in order to agree with AA numbering in PDB file. TMhelices=3.
pir_number:
Swiss_Prot_entry:PSAL_SYNEN
Swiss_Prot_number:P25902
Swiss_Prot_gene:PSAL,TLR2404
Swiss_Prot_name:Photosystem I subunit XI
PDB_title:PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI
PDB_Identifier:1JB0
N_terminal:in
number_tmsegs:3
tm_segments:A.43,65;B.74,99;C.114,140
sequence:AEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLIGPWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQFTAGFFVGAMGSAFVAFFLLENFLVVDGIMTGLFN*
>3D_helix;105
protein_name:photosystem I M subunit (Synechococcus elongatus)
file_name:PS_I_PsaM.txt
entry_date:6jul01
refman_number:19835,16396,19598,16394,13836,20928
endnote_number:
author:Jordan,P., Fromme,P., Witt,H.T., Klukas,O., Saenger,W., Krauss,N. (2001) [Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution] {Nature, 411, 909-917}
remarks:Stroma=in. Sequence from Swiss-Prot. TMhelices=1.
pir_number:
Swiss_Prot_entry:PSAM_SYNEL
Swiss_Prot_number:P25903
Swiss_Prot_gene:PSAM,TSR0197
Swiss_Prot_name:Photosystem I reaction centre subunit XII
PDB_title:PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII
PDB_Identifier:1JB0
N_terminal:out
number_tmsegs:1
tm_segments:A.6,30
sequence:MALTDTQVYVALVIALLPAVLAFRLSTELYK*
>3D_helix;106
protein_name:photosystem I X subunit (Synechococcus elongatus)
file_name:PS_I_PsaX.txt
entry_date:6jul01
refman_number:19835,16396,19598,16394,13836,20928
endnote_number:
author:Jordan,P., Fromme,P., Witt,H.T., Klukas,O., Saenger,W., Krauss,N. (2001) [Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution] {Nature, 411, 909-917}
remarks:Stroma=in. Sequence from TrEMBL. TMhelices=1.
pir_number:
Swiss_Prot_entry:Q8DKP6
Swiss_Prot_number:Q8DKP6
Swiss_Prot_gene:TSR0813
Swiss_Prot_name:Photosystem I 4.8K protein
PDB_title:X PHOTOSYSTEM I SUBUNIT PSAX
PDB_Identifier:1JB0
N_terminal:in
number_tmsegs:1
tm_segments:A.11,31
sequence:ATKSAKPTYAFRTFWAVLLLAINFLVAAYYFAAAA*
>3D_helix;200
protein_name:photosystem II core light harvesting protein (Thermosynechococcus elongatus)
file_name:PSII_CP47_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain B in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:Q8DIQ1_SYNEL
Swiss_Prot_number:Q8DIQ1
Swiss_Prot_gene:psbB
Swiss_Prot_name:Photosystem II core light harvesting protein
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:in
number_tmsegs:6
tm_segments:A.16,44;B.93,112;C.135,155;D.196,214;E.236,258;F.447,472
sequence:MGLPWYRVHTVLINDPGRLIAAHLMHTALVAGWAGSMALYELATFDPSDPVLNPMWRQGMFVLPFMARLGVTGSWSGWSITGETGIDPGFWSFEGVALAHIVLSGLLFLAACWHWVYWDLELFRDPRTGEPALDLPKMFGIHLFLAGLLCFGFGAFHLTGLFGPGMWVSDPYGLTGSVQPVAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIAGLFHILVRPPQRLYKALRMGNIETVLSSSIAAVFFAAFVVAGTMWYGSATTPIELFGPTRYQWDSSYFQQEINRRVQASLASGATLEEAWSAIPEKLAFYDYIGNNPAKGGLFRTGPMNKGDGIAQAWKGHAVFRNKEGEELFVRRMPAFFESFPVILTDKNGVVKADIPFRRAESKYSFEQQGVTVSFYGGELNGQTFTDPPTVKSYARKAIFGEIFEFDTETLNSDGIFRTSPRGWFTFAHAVFALLFFFGHIWHGARTLFRDVFSGIDPELSPEQVEWGFYQKVGDVTTRRKEAV*
>3D_helix;201
protein_name:Photosystem II CP43 protein (Thermosynechococcus elongatus)
file_name:PSII_CP43_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain C in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:Q8DIF8_SYNEL
Swiss_Prot_number:Q8DIF8
Swiss_Prot_gene:psbC
Swiss_Prot_name:Photosystem II CP43 protein
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:in
number_tmsegs:6
tm_segments:A.49,74;B.111,134;C.154,177;D.231,253;E.268,291;F.423,446
sequence:MKTLSSQKRYSPVVTLSSNSIFATNRDQESSGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMTLFELAHFIPEKPMYEQGLILIPHIATLGWGVGPGGEVVDTFPFFVVGVVHLISSAVLGFGGVYHAIRGPETLEEYSSFFGYDWKDKNKMTTILGFHLIVLGIGALLLVAKAMFFGGLYDTWAPGGGDVRVITNPTLDPRVIFGYLLKSPFGGEGWIVSVNNLEDVVGGHIWIGLICIAGGIWHILTTPFGWARRAFIWSGEAYLSYSLGALSMMGFIATCFVWFNNTVYPSEFYGPTGPEASQAQAMTFLIRDQKLGANVGSAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFRGPWLEPLRGPNGLDLNKIKNDIQPWQERRAAEYMTHAPLGSLNSVGGVATEINSVNFVSPRSWLATSHFVLAFFFLVGHLWHAGRARAAAAGFEKGIDRESEPVLSMPSLD*
>3D_helix;203
protein_name:Photosystem II Cytochrome b559 alpha subunit (Thermosynechococcus elongatus)
file_name:PSII_cyt.b559-alpha_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain E in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBE_SYNEL
Swiss_Prot_number:Q8DIP0
Swiss_Prot_gene:psbE
Swiss_Prot_name:Cytochrome b559 alpha subunit
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:in
number_tmsegs:1
tm_segments:A.16,38
sequence:AGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPDSYYAQEQRSIPLVTDRFEAKQQVETFLEQLK*
>3D_helix;204
protein_name:Photosystem II Cytochrome b559 beta subunit(Thermosynechococcus elongatus)
file_name:PSII_cyt.b559-beta_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain F in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBF_SYNEL
Swiss_Prot_number:Q8DIN9
Swiss_Prot_gene:psbF
Swiss_Prot_name:Cytochrome b559 subunit beta
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:in
number_tmsegs:1
tm_segments:A.16,39
sequence:MTSNTPNQEPVSYPIFTVRWVAVHTLAVPTIFFLGAIAAMQFIQR*
>3D_helix;202
protein_name:Photosystem II D2 protein (Thermosynechococcus elongatus)
file_name:PSII_D2_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain D in PDB file. TM C and E contains of two helices. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:Q8CM25_SYNEL
Swiss_Prot_number:Q8CM25
Swiss_Prot_gene:psbD2
Swiss_Prot_name:Photosystem II reaction center D2 protein
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:in
number_tmsegs:5
tm_segments:A.34,54;B.110,131;C.142,157;D.195,220;E.265,289
sequence:MTIAIGRAPAERGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLCAIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL*
>3D_helix;205
protein_name:Photosystem II PsbH protein(Thermosynechococcus elongatus)
file_name:PSII_PsbH_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain H in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBH_SYNEL
Swiss_Prot_number:Q8DJ43
Swiss_Prot_gene:psbH
Swiss_Prot_name:photosystem II reaction center protein H
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:in
number_tmsegs:1
tm_segments:A.27,48
sequence:MARRTWLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFLVFLLIILEIYNSTLILDGVNVSWKALG*
>3D_helix;206
protein_name:Photosystem II PsbI protein (Thermosynechococcus elongatus)
file_name:PSII_PsbI_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain I in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBI_SYNEL
Swiss_Prot_number:Q8DJZ6
Swiss_Prot_gene:psbI
Swiss_Prot_name:Photosystem II reaction center protein I
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:out
number_tmsegs:1
tm_segments:A.3,20
sequence:METLKITVYIVVTFFVLLFVFGFLSGDPARNPKRKDLE*
>3D_helix;207
protein_name:Photosystem II PsbJ protein (Thermosynechococcus elongatus)
file_name:PSII_PsbJ_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain J in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBJ_SYNEL
Swiss_Prot_number:P59087
Swiss_Prot_gene:psbJ
Swiss_Prot_name:Photosystem II reaction center protein J
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:in
number_tmsegs:1
tm_segments:A.13,30
sequence:MMSEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL*
>3D_helix;208
protein_name:Photosystem II PsbK protein (Thermosynechococcus elongatus)
file_name:PSII_PsbK_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from PDB, chain K. In Swiss-Prot file there is aditional 9 aa at the beginning so res#1 in PBD file corresponds to res#10 in Swiss-Prot file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBK_SYNEL
Swiss_Prot_number:Q9F1K9
Swiss_Prot_gene:psbK
Swiss_Prot_name:Photosystem II reaction center protein K
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:out
number_tmsegs:1
tm_segments:A.4,33
sequence:KLPEAYAIFDPLVDVLPVIPVLFLALAFVWQAAVGFR*
>3D_helix;209
protein_name:Photosystem II PsbL protein (Thermosynechococcus elongatus)
file_name:PSII_PsbL_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain L in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBL_SYNEL
Swiss_Prot_number:Q8DIN8
Swiss_Prot_gene:psbL
Swiss_Prot_name:Photosystem II reaction center protein L
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:in
number_tmsegs:1
tm_segments:A.14,36
sequence:MEPNPNRQPVELNRTSLYLGLLLILVLALLFSSYFFN*
>3D_helix;210
protein_name:Photosystem II PsbM protein (Thermosynechococcus elongatus)
file_name:PSII_PsbM_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain M in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBM_SYNEL
Swiss_Prot_number:Q8DHA7
Swiss_Prot_gene:psbM
Swiss_Prot_name:Photosystem II reaction center protein M
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:out
number_tmsegs:1
tm_segments:A.6,29
sequence:MEVNQLGLIATALFVLVPSVFLIILYVQTESQQKSS*
>3D_helix;213
protein_name:Photosystem II PsbN protein (Thermosynechococcus elongatus)
file_name:PSII_PsbN_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain N in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBN_SYNEL
Swiss_Prot_number:Q8DJ42
Swiss_Prot_gene:psbN
Swiss_Prot_name:Photosystem II reaction center protein N
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:out
number_tmsegs:1
tm_segments:A.2,30
sequence:MEPATVLSIALAAVCIGVTGYSIYLSFGPPSKELADPFDDHED
>3D_helix;211
protein_name:Photosystem II PsbT protein (Thermosynechococcus elongatus)
file_name:PSII_PsbT_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain T in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBT_SYNEL
Swiss_Prot_number:Q8DIQ0
Swiss_Prot_gene:psbT
Swiss_Prot_name:photosystem II reaction center protein T
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:out
number_tmsegs:1
tm_segments:A.5,22
sequence:METITYVFIFACIIALFFFAIFFREPPRITKK*
>3D_helix;212
protein_name:Photosystem II PsbX protein (Thermosynechococcus elongatus)
file_name:PSII_PsbX_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain X in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:Q8DHE6_SYNEL
Swiss_Prot_number:Q8DHE6
Swiss_Prot_gene:psbX
Swiss_Prot_name:photosystem II PsbX protein
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:out
number_tmsegs:1
tm_segments:A.15,43
sequence:MIQSASSLLLTITPSLKGFFIGLLSGAVVLGLTFAVLIAISQIDKVQRSL*
>3D_helix;214
protein_name:Photosystem II PsbZ protein (Thermosynechococcus elongatus)
file_name:PSII_PsbZ_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain Z in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:
Swiss_Prot_entry:PSBZ_SYNEL
Swiss_Prot_number:Q8DHJ2
Swiss_Prot_gene:psbZ
Swiss_Prot_name:Photosystem II reaction center protein Z
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:out
number_tmsegs:2
tm_segments:A.2,19;B.33,56
sequence:MTILFQLALAALVILSFVMVIGVPVAYASPQDWDRSKQLIFLGSGLWIALVLVVGVLNFFVV*
>3D_helix;199
protein_name:Photosystem II Q(B) protein (Thermosynechococcus elongatus)
file_name:PSII_Psb1_Thermo_elong.txt
entry_date:15july04
refman_number:21418
endnote_number:
author:Ferreira,K.N., Iverson,T.M., Maghlaoui,K., Barber,J., Iwata,S. (2004) [Architecture of the photosynthetic oxygen-evolving center] {Science, 303, 1831-1838}
remarks:Sequence from Swiss-Prot. This corresponds to chain A in PDB file. See also 1FE1(earlier lower resolution structure)and 2AXT(later higher resolution structure). Stroma=in.
pir_number:S26586
Swiss_Prot_entry:PSBA1_SYNEL
Swiss_Prot_number:P0A444
Swiss_Prot_gene:psbA1
Swiss_Prot_name:Photosystem Q(B) protein
PDB_title:Architecture of the photosynthetic oxygen evolving center
PDB_Identifier:1S5L
N_terminal:in
number_tmsegs:5
tm_segments:A.34,54;B.111,136;C.145,158;D.199,221;E.268,295
sequence:MTTTLQRRESANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQWELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGALFCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFTALGISTMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEVMHERNAHNFPLDLASAESAPVAMIAPSING*
>3D_helix;179
protein_name:reaction center chain H (Thermochromatium tepidum)
file_name:PSRC_TT_H.txt
entry_date:23jan04
refman_number:21300,21301
endnote_number:
author:Nogi,T., Fathir,I., Kobayashi,M., Nozawa,T., Miki,K. (2000) [Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: Thermostability and electron transfer] {Proc Nat Acad Sci USA, 97, 13561-13566}
remarks:Sequence from PDB. TMhelices=1.
pir_number:
Swiss_Prot_entry:Q93RD8
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Photosynthetic reaction center, H subunit
PDB_Identifier:1EYS
N_terminal:out
number_tmsegs:1
tm_segments:A.11,33
sequence:MPAGITHYIDAAQITIWAFWLFFFGLIIYLRREDKREGYPLDSNRTERSGGRYKVVGFPDLPDPKTFVLPHNGGTVVAPRVEAPVAVNATPFSPAPGSPLVPNGDPMLSGFGPAASPDRPKHCDLTFEGLPKIVPMRVAKEFSIAEGDPDPRGMTVVGLDGEVAGTVSDVWVDRSEPQIRYLEVEVAANKKKVLLPIGFSRFDKKARKVKVDAIKAAHFANVPTLSNPDQVTLYEEDKVCAYYAGGKLYATAERAGPLL*
>3D_helix;180
protein_name:reaction center chain L (Thermochromatium tepidum)
file_name:PSRC_TT_L.txt
entry_date:23jan04
refman_number:21300,21301
endnote_number:
author:Nogi,T., Fathir,I., Kobayashi,M., Nozawa,T., Miki,K. (2000) [Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: Thermostability and electron transfer] {Proc Nat Acad Sci USA, 97, 13561-13566}
remarks:Sequence from PDB. TMhelices=5
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Photosynthetic reaction center, L subunit
PDB_Identifier:1EYS
N_terminal:in
number_tmsegs:5
tm_segments:A.33,55;B.93,119;C.124,147;D.179,205;E.234,258
sequence:AMLSFEKKYRVRGGTLIGGDLFDFWVGPFYVGFFGVVGFCFTLLGVLLIVWGATIGPTGPTSDLQTYNLWRISIAPPDLSYGLRMAPLTEGGLWQIITICAAGAFISWALREVEICRKLGIGFHVPFAFSFAIGAYLVLVFVRPLLMGAWGHGFPYGILSHLDWVSNVGYQFLHFHYNPAHMLAISFFFTNCLALSMHGSLILSVTNPQRGEPVKTSEHENTFFRDIVGYSIGALAIHRLGLFLALSAAFWSAVCILISGPFWTRGWPEWWNWWLELPLW*
>3D_helix;181
protein_name:reaction center chain M (Thermochromatium tepidum)
file_name:PSRC_TT_M.txt
entry_date:23jan04
refman_number:21300,21301
endnote_number:
author:Nogi,T., Fathir,I., Kobayashi,M., Nozawa,T., Miki,K. (2000) [Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: Thermostability and electron transfer] {Proc Nat Acad Sci USA, 97, 13561-13566}
remarks:Sequence from PDB. TMhelices=5.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Photosynthetic reaction center, M subunit
PDB_Identifier:1EYS
N_terminal:in
number_tmsegs:5
tm_segments:A.54,77;B.112,134;C.144,167;D.196,224;E.265,284
sequence:PEYQNIFTAVQVRAPAYPGVPLPKGNLPRIGRPIFSYWLGKIGDAQIGPIYLGLTGTLSIFFGLVAISIIGFNMLASVHWDVFQFLKHFFWLGLEPPPPQYGLRIPPLSEGGWWLIAGLFLTLSILLWWVRTYKRAEALGMSQHLSWAFAAAIFFYLVLGFIRPVMMGSWAKAVPFGIFPHLDWTAAFSIRYGNLYYNPFHMLSIAFLYGSALLFAMHGATILSVSRFGGDREIDQITHRGTAAEGAALFWRWTMGFNATMESIHRWAWWCAVLTVITAGIGILLSGTVVDNWYLWAVKHGMAPAYPEVVTAVNPYETAAEVMQ*
>3D_helix;63
protein_name:Reaction center. Chain H (R. sphaeroides)
file_name:PSRC-RS-H.txt
entry_date:8Oct98
refman_number:1152,3551,1192,5719,5111,13834,13835,12247,1989,1980,2134,12155
endnote_number:
author:Allen,J.P., Feher,G., Yeates,T.O., Komiya,H., Rees,D.C. (1987) [Structure of the reaction center from Rhodobacter sphaeroides R-26: The protein subunits] {Proc Natl Acad Sci USA, 84, 6162-6166}
remarks:Sequence from Swiss-Prot. TMhelices=1.
pir_number:A26538
Swiss_Prot_entry:RCEH_RHOSH
Swiss_Prot_number:P11846
Swiss_Prot_gene:PUHA
Swiss_Prot_name:Reaction center protein H chain
PDB_title:Photosynthetic reaction center from (Rhodobacter sphaeroides)
PDB_Identifier:2RCR,4RCR
N_terminal:out
number_tmsegs:1
tm_segments:A.13,36
sequence:MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRKSVVAAMLAEYA*
>3D_helix;33
protein_name:Reaction center. Chain H (R. viridis)
file_name:PSRC-RV-H.txt
entry_date:27may98
refman_number:1623,13870
endnote_number:
author:Deisenhofer,J., Epp,O., Miki,K., Huber,R., Michel,H. (1985) [Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 Å resolution] {Nature, 318, 618-624}
remarks:Sequence from Swiss-Prot. TMhelices=1.
pir_number:A22841
Swiss_Prot_entry:RCEH_RHOVI
Swiss_Prot_number:P06008
Swiss_Prot_gene:PUHA
Swiss_Prot_name:Reaction center protein H chain
PDB_title:photosynthetic reaction center
PDB_Identifier:1PRC
N_terminal:out
number_tmsegs:1
tm_segments:A.12,37
sequence:MYHGALAQHLDIAQLVWYAQWLVIWTVVLLYLRREDRREGYPLVEPLGLVKLAPEDGQVYELPYPKTFVLPHGGTVTVPRRRPETRELKLAQTDGFEGAPLQPTGNPLVDAVGPASYAERAEVVDATVDGKAKIVPLRVATDFSIAEGDVDPRGLPVVAADGVEAGTVTDLWVDRSEHYFRYLELSVAGSARTALIPLGFCDVKKDKIVVTSILSEQFANVPRLQSRDQITLREEDKVSAYYAGGLLYATPERAESLL*
>3D_helix;64
protein_name:Reaction center. Chain L (R. sphaeroides)
file_name:PSRC-RS-L.txt
entry_date:8Oct98
refman_number:1152,3551,1192,5719,5111,13834,13835,12247,1989,1980,2134,12155
endnote_number:
author:Allen,J.P., Feher,G., Yeates,T.O., Komiya,H., Rees,D.C. (1987) [Structure of the reaction center from Rhodobacter sphaeroides R-26: The protein subunits] {Proc Natl Acad Sci USA, 84, 6162-6166}
remarks:Sequence from Swiss-Prot. TMhelices=5.
pir_number:WNRFLS
Swiss_Prot_entry:RCEL_RHOSH
Swiss_Prot_number:P02954
Swiss_Prot_gene:PUFL
Swiss_Prot_name:Reaction center protein L chain
PDB_title:Photosynthetic reaction center from (Rhodobacter sphaeroides)
PDB_Identifier:2RCR,4RCR
N_terminal:in
number_tmsegs:5
tm_segments:A.32,55;B.84,111;C.115,140;D.170,199;E.225,251
sequence:ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWNPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFAFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFFFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSAVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING*
>3D_helix;34
protein_name:Reaction center. Chain L (R. viridis)
file_name:PSRC-RV-L.txt
entry_date:27may98
refman_number:1623,13870
endnote_number:
author:Deisenhofer,J., Epp,O., Miki,K., Huber,R., Michel,H. (1985) [Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 Å resolution] {Nature, 318, 618-624}
remarks:Sequence from Swiss-Prot. TMhelices=5.
pir_number:A25102
Swiss_Prot_entry:RCEL_RHOVI
Swiss_Prot_number:P06009
Swiss_Prot_gene:PUFL
Swiss_Prot_name:Reaction center protein L chain
PDB_title:photosynthetic reaction center
PDB_Identifier:1PRC
N_terminal:in
number_tmsegs:5
tm_segments:A.32,55;B.84,112;C.115,140;D.170,199;E.225,251
sequence:ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS*
>3D_helix;65
protein_name:Reaction center. Chain M (R. sphaeroides)
file_name:PSRC-RS-M.txt
entry_date:8Oct98
refman_number:1152,3551,1192,5719,5111,13834,13835,12247,1989,1980,2134,12155
endnote_number:
author:Allen,J.P., Feher,G., Yeates,T.O., Komiya,H., Rees,D.C. (1987) [Structure of the reaction center from Rhodobacter sphaeroides R-26: The protein subunits] {Proc Natl Acad Sci USA, 84, 6162-6166}
remarks:Sequence from Swiss-Prot. TMhelices=5.
pir_number:WNRFMS
Swiss_Prot_entry:RCEM_RHOSH
Swiss_Prot_number:P02953
Swiss_Prot_gene:PUFM
Swiss_Prot_name:Reaction center protein M chain
PDB_title:Photosynthetic reaction center from (Rhodobacter sphaeroides)
PDB_Identifier:2RCR,4RCR
N_terminal:in
number_tmsegs:5
tm_segments:A.52,77;B.110,139;C.142,167;D.197,224;E.259,285
sequence:AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQNHGMAPLN*
>3D_helix;35
protein_name:Reaction center. Chain M (R. viridis)
file_name:PSRC-RV-M.txt
entry_date:27may98
refman_number:1623,13870
endnote_number:
author:Deisenhofer,J., Epp,O., Miki,K., Huber,R., Michel,H. (1985) [Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 Å resolution] {Nature, 318, 618-624}
remarks:Sequence from Swiss-Prot. TMhelices=5.
pir_number:B25102
Swiss_Prot_entry:RCEM_RHOVI
Swiss_Prot_number:P06010
Swiss_Prot_gene:PUFM
Swiss_Prot_name:Reaction center protein M chain
PDB_title:photosynthetic reaction center
PDB_Identifier:1PRC
N_terminal:in
number_tmsegs:5
tm_segments:A.52,78;B.110,139;C.142,167;D.197,225;E.259,285
sequence:ADYQTIYTQIQARGPHITVSGEWGDNDRVGKPFYSYWLGKIGDAQIGPIYLGASGIAAFAFGSTAILIILFNMAAEVHFDPLQFFRQFFWLGLYPPKAQYGMGIPPLHDGGWWLMAGLFMTLSLGSWWIRVYSRARALGLGTHIAWNFAAAIFFVLCIGCIHPTLVGSWSEGVPFGIWPHIDWLTAFSIRYGNFYYCPWHGFSIGFAYGCGLLFAAHGATILAVARFGGDREIEQITDRGTAVERAALFWRWTIGFNATIESVHRWGWFFSLMVMVSASVGILLTGTFVDNWYLWCVKHGAAPDYPAYLPATPDPASLPGAPK*
>3D_helix;66
protein_name:rhodopsin (bovine)
file_name:Rhodopsin-bov.txt
entry_date:8oct98
refman_number:19008,12836,13790,12169,9140,12372
endnote_number:
author:Palczewski,K., Kumasaka,T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Le Trong, I., Teller,D. C., Okada, T., Stenkamp, R. E., Yamamoto, M., Miyano, M. (2000) [Crystal structure of rhodopsin: A G protein-coupled receptor] {Science, 289, 739-745}
remarks:Sequence from Swiss-Prot. TMhelices=7.
pir_number:OOBO
Swiss_Prot_entry:OPSD_BOVIN
Swiss_Prot_number:P02699
Swiss_Prot_gene:RHO
Swiss_Prot_name:Rhodopsin
PDB_title:crystal structure of bovine rhodopsin - Chain A, B
PDB_Identifier:1F88
N_terminal:out
number_tmsegs:7
tm_segments:A.35,64;B.71,100;C.107,139;D.151,173;E.200,225;F.247,277;G.286,306
sequence:MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA*
>3D_helix;242
protein_name:Rhomboid peptidase (Haemophilus influenzae)
file_name:GlpG_Hae_influenzae.txt
entry_date:17jan07
refman_number:
endnote_number:22366
author:Lemieux,M.J., Fischer,S.J., Cherney,M.M., Bateman,K.S., James,M.N.G. (2007) [The crystal structure of the rhomoboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis] {Proc Natl Acad Sci USA, 104, 750-754}
remarks:Sequence from Swiss-Prot. TM E is unusual in that it is not fully alpha helical but rather is deformed. check orginal article for details.
pir_number:I64081
Swiss_Prot_entry:GLPG_HAEIN
Swiss_Prot_number:P44783
Swiss_Prot_gene:glpG
Swiss_Prot_name:Protein glpG homolog
PDB_title:Crystal structure of GlpG, Rhomboid Peptidase from Haemophilus influenzae
PDB_Identifier:2NR9
N_terminal:in
number_tmsegs:6
tm_segments:A.10,26;B.63,84;C.86,108;D.116,131;E.137,156;F.166,191
sequence:MKNFLAQQGKITLILTALCVLIYLAQQLGFEDDIMYLMHYPAYEEQDSEVWRYISHTLVHLSNLHILFNLSWFFIFGGMIERTFGSVKLLMLYVVASAITGYVQNYVSGPAFFGLSGVVYAVLGYVFIRDKLNHHLFDLPEGFFTMLLVGIALGFISPLFGVEMGNAAHISGLIVGLIWGFIDSKLRKNSLE*
>3D_helix;243
protein_name:Rhomboid Protease GlpG (Escherichia coli)
file_name:GlpG_Ecoli.txt
entry_date:17jan07
refman_number:
endnote_number:22277
author:Wang,Y., Zhang,Y., Ha,Y. (2006) [Crystal structure of a rhomboid family intramembrane protease] {Nature, 444, 179-183}
remarks:Sequence from Swiss-Prot.
pir_number:
Swiss_Prot_entry:P09391
Swiss_Prot_number:GLPG_ECOLI
Swiss_Prot_gene:glpG
Swiss_Prot_name:Protein glpG
PDB_title:Crystal structure of GlpG
PDB_Identifier:2IC8
N_terminal:out
number_tmsegs:6
tm_segments:A.95,114;B.148,169;C.171,193;D.201,217;E.227,241;F.251,268
sequence:MLMITSFANPRVAQAFVDYMATQGVILTIQQHNQSDVWLADESQAERVRAELARFLENPADPRYLAASWQAGHTGSGLHYRRYPFFAALRERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNARKRK*
>3D_helix;165
protein_name:SecY complex, alpha subunit (Methanococcus jannaschii)
file_name:SecY_alpha_Methjann.txt
entry_date:30dec03
refman_number:21231
endnote_number:
author:Van den Berg,B., Clemons,W.M.,Jr., Collinson,I., Modis,Y., Hartmann,E., Harrison,S.C., Rapoport,T.A. (2003) [X-ray structure of a protein-conducting channel] {Nature, 427, 36-44}
remarks:SecY protein. Cytoplasm = in. Sequence is from Swiss-Prot with Met1 removed so that it corresponds to the sequence in the PDB file. TMhelices=10.
pir_number:
Swiss_Prot_entry:SECY_METJA
Swiss_Prot_number:Q60175
Swiss_Prot_gene:SECY,MJ0478
Swiss_Prot_name:Preprotein translocase secY subunit
PDB_title:Preprotein translocase Secy subunit
PDB_Identifier:1RHZ,1RH5
N_terminal:in
number_tmsegs:10
tm_segments:A.22,45;B.74,90;C.101,129;D.137,164;E.169,202;F.207,229;G.254,276;H.313,333;I.364,396;J.400,425
sequence:KKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWQTITASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFRKSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLREKVSELHPAIAKLLNK*
>3D_helix;166
protein_name:SecY complex, beta subunit (Methanococcus jannaschii)
file_name:SecY_beta_Methjann.txt
entry_date:30dec03
refman_number:21231
endnote_number:
author:Van den Berg,B., Clemons,W.M.,Jr., Collinson,I., Modis,Y., Hartmann,E., Harrison,S.C., Rapoport,T.A. (2003) [X-ray structure of a protein-conducting channel] {Nature, 427, 36-44}
remarks:SecG protein equivalent. Cytoplasm = in. Sequence from PDB. There is no sequence in Swiss-Prot. TMhelices=1.
pir_number:
Swiss_Prot_entry:
Swiss_Prot_number:
Swiss_Prot_gene:
Swiss_Prot_name:
PDB_title:Preprotein Translocase Secy Subunit
PDB_Identifier:1RHZ,1RH5
N_terminal:in
number_tmsegs:1
tm_segments:A.30,48
sequence:MSKREETGLATSAGLIRYMDETFSKIRVKPEHVIGVTVAFVIIEAILTYGRFL*
>3D_helix;167
protein_name:SecY complex, gamma subunit (Methanococcus jannaschii)
file_name:SecY_gamma_Methjann.txt
entry_date:30dec03
refman_number:21231
endnote_number:
author:Van den Berg,B., Clemons,W.M.,Jr., Collinson,I., Modis,Y., Hartmann,E., Harrison,S.C., Rapoport,T.A. (2003) [X-ray structure of a protein-conducting channel] {Nature, 427, 36-44}
remarks:SecE protein. Cytoplasm = in. Sequence from Swiss-Prot, with Met1 removed so that sequence corresponds to that in PDB. TMhelices=1.
pir_number:
Swiss_Prot_entry:SECE_METJA
Swiss_Prot_number:Q57817
Swiss_Prot_gene:SECE, MJ0371
Swiss_Prot_name:Preprotein translocase secE subunit
PDB_title:Preprotein Translocase Secy subunit
PDB_Identifier:1RHZ,1RH5
N_terminal:in
number_tmsegs:1
tm_segments:A.30,64
sequence:KTDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPATYIKGILKPPTTPRV*
>3D_helix;222
protein_name:sensory rhodopsin (Anabaena)
file_name:sensory_rhodopsin_Anabaena.txt
entry_date:08mar05
refman_number:21688
endnote_number:
author:Vogeley,L., Sineshchekov,O.A., Trivedi,V.D., Sasaki,J., Spudich,J.L., Luecke,H. (2004) [Anabaena sensory rhodopsin: A photochromic color sensor at 2.0 Å] {Science, 306, 1390-1393}
remarks:Sequence from PDB
pir_number:AF2201
Swiss_Prot_entry:Q8YSC4_ANASP
Swiss_Prot_number:Q8YSC4
Swiss_Prot_gene:alr3165
Swiss_Prot_name:bacteriorhodopsin
PDB_title:Anabaena sensory rhodopsin
PDB_Identifier:1XIO
N_terminal:out
number_tmsegs:7
tm_segments:A.3,26;B.34,56;C.72,91;D.99,121;E.125,147;F.159,185;G.195,209
sequence:MNLESLLHWIYVAGMTIGALHFWSLSRNPRGVPQYEYLVAMFIPIWSGLAYMAMAIDQGK VEAAGQIAHYARYIDWMVTTPLLLLSLSWTAMQFIKKDWTLIGFLMSTQIVVITSGLIADLSERDWVRYLWYICGVCAFLIILWGIWNPLRAKTRTQSSELANLYDKLVTYFTVLWIGYPIVWIIGPSGFGWINQTIDTFLFCLLPFFSKVGFSFLDLHGLRNLNDSRQTTGDRFAENTLQFVENITLFANSRRQQSRRRV*
>3D_helix;113
protein_name:sensory rhodopsin II (N. pharaonis)
file_name:sensor_rhodop_II.txt
entry_date:16July02
refman_number:19958,20398
endnote_number:
author:Royant,A., Nollert,P., Edman,K., Neutze,R., Landau,E.M., Pebay-Peyroula,E., Navarro,J. (2001) [X-ray structure of sensory rhodopsin II at 2.1-Å resolution] {Proc Natl Acad Sci USA, 98, 10131-10136}
remarks:Sequence is from Swiss-Prot. TMhelices=7.
pir_number:S55300
Swiss_Prot_entry:BACT_NATPH
Swiss_Prot_number:P42196
Swiss_Prot_gene:SOP2,SOPII
Swiss_Prot_name:Sensory rhodopsin II
PDB_title:Sensory Rhodopsin II
PDB_Identifier:1H68,1JGJ
N_terminal:out
number_tmsegs:7
tm_segments:A.3,26;B.33,56;C.70,