Welcome to MPtopo, a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. If you publish work that used MPtopo, please cite Jayasinghe et al. (2001) Protein Sci. 10:455-458.

MPtopo has now been integrated with mpstruc. Unlike the previous version, MPtopo now includes only proteins of known 3D structure; the 1D_Helix entries, whose TM helices were identified by experimental techniques such as gene fusion, have been removed.

MPtopo Querier is no longer available as a separate application, but does remain integral to MPEx. The 'text search' below is similar to 'text search' in mpstruc. We will eventually add additional search capabilities found in the old MPtopo Querier. In addition, we will provide the same capabilities found on the mpstruc page, such as XML representations.

MPtopo currently contains a total of 165 proteins with 949 TM segments.

Latest new protein topology entered: 07 Feb 2007 at 00:00 PST.
Last MPtopo database update: 06 Aug 2014 at 15:23 PDT

Summary of MPtopo Data*
Characteristic Beta-Barrel TM Proteins Alpha-Helical TM Proteins
*Not included in this table (but included in the database) are monotopic proteins and proteins with complex topologies, such as chloride channels, whose TM segments are not easily classified. A list of these proteins is available here (coming soon).
Number of  Proteins/Protein Subunits 25 119
Number of  total residues 10294 27312
Number of residues in TM segments 4207 11848
Number of  total TM segments 334 455
Average TM segment length 12±3 26±5
TM segment length range 6-23 10-48
 
XML Representations

An XML representation provides a convenient machine or human readable format of the portion of the data table that has been made visible, and allows you to build software tools to consume it as you see fit. You can use the URLs adjacent to the buttons below to access the same view the corresponding button provides.

This button generates an XML representation of the currently visible portion of the table.

http://blanco.biomol.uci.edu/mpstruc/mptopo/mptopoTblXml
http://blanco.biomol.uci.edu/mpstruc/mptopo/mptopoMonotopicTblXml
http://blanco.biomol.uci.edu/mpstruc/mptopo/mptopoBetaBrlTblXml
http://blanco.biomol.uci.edu/mpstruc/mptopo/mptopoAlphaHlxTblXml

If your browser doesn’t directly display a nicely formatted XML page, it should provide a "view page source" menu selection that will. It should also provide a "save page" option so that you can download the XML formatted data.

If you’re not familiar with XML and how to use it, a good source of information is available here.

NOTES:

Generated XML includes the following Document Type Definition (DTD):

<!DOCTYPE mptopo [
  <!ELEMENT mptopo (caption,groups*)>
  <!ATTLIST mptopo createdBy CDATA #REQUIRED>
  <!ATTLIST mptopo maintainedBy CDATA #REQUIRED>
  <!ATTLIST mptopo copyright CDATA #REQUIRED>
  <!ATTLIST mptopo url CDATA #REQUIRED>
  <!ATTLIST mptopo lastNewMptopoProteinDate CDATA #REQUIRED>
  <!ATTLIST mptopo lastDatabaseEditDate CDATA #REQUIRED>
  <!ATTLIST mptopo timeStamp CDATA #REQUIRED>
  <!ELEMENT caption (#PCDATA)>
  <!ELEMENT groups (group*)>
  <!ELEMENT group (name,mptopoProteins?,subgroups)>
  <!ELEMENT subgroups (subgroup*)>
  <!ELEMENT subgroup (name,mptopoProteins)>
  <!ELEMENT name (#PCDATA)>
  <!ELEMENT mptopoProteins (mptopoProtein*)>
  <!ELEMENT mptopoProtein (proteinName,species,taxonomicDomain,remarks,pirNumber,
                           uniprotEntry,uniprotNumber,uniprotGene,uniprotName,
                           pdbTitle,pdbCodes,
                           nTerminal,sequence,complexTopology,tmSegments,
                           bibliography,secondaryBibliographies)>
  <!ELEMENT proteinName (#PCDATA)>
  <!ELEMENT species (#PCDATA)>
  <!ELEMENT taxonomicDomain (#PCDATA)>
  <!ELEMENT remarks (#PCDATA)>
  <!ELEMENT pirNumber (#PCDATA)>
  <!ELEMENT uniprotEntry (#PCDATA)>
  <!ELEMENT uniprotNumber (#PCDATA)>
  <!ELEMENT uniprotGene (#PCDATA)>
  <!ELEMENT uniprotName (#PCDATA)>
  <!ELEMENT pdbTitle (#PCDATA)>
  <!ELEMENT pdbCodes (pdbCode*)>
  <!ELEMENT pdbCode (#PCDATA)>
  <!ELEMENT nTerminal (#PCDATA)>
  <!ELEMENT sequence (#PCDATA)>
  <!ELEMENT complexTopology (#PCDATA)>
  <!ELEMENT tmSegments (tmSegment*)>
  <!ELEMENT tmSegment (segLabel,beginIndex,endIndex)>
  <!ELEMENT segLabel (#PCDATA)>
  <!ELEMENT beginIndex (#PCDATA)>
  <!ELEMENT endIndex (#PCDATA)>
  <!ELEMENT bibliography (pubMedId,authors,year,title,journal,volume,issue,pages,doi,notes)>
  <!ELEMENT pubMedId (#PCDATA)>
  <!ELEMENT authors (#PCDATA)>
  <!ELEMENT year (#PCDATA)>
  <!ELEMENT title (#PCDATA)>
  <!ELEMENT journal (#PCDATA)>
  <!ELEMENT volume (#PCDATA)>
  <!ELEMENT issue (#PCDATA)>
  <!ELEMENT pages (#PCDATA)>
  <!ELEMENT doi (#PCDATA)>
  <!ELEMENT notes (#PCDATA)>
  <!ELEMENT secondaryBibliographies (bibliography*)>
]>

 
Membrane Protein Topology Database
Protein
UniProt ID PDB ID Reference
(links are to PubMed)
MONOTOPIC MEMBRANE PROTEINS
TRANSMEMBRANE PROTEINS: BETA-BARREL
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL