When referencing this page, please use this url: https://blanco.biomol.uci.edu/mpstruc/

mpstruc is a curated database of membrane proteins of known 3D structure. To be included in the database, a structure must be available in the RSCB Protein Data Bank (PDB) and have been published in a peer reviewed journal. The database is manually curated based upon on-going literature surveys. Because of the labor involved, new structures are not posted until they are released by the PDB and the complete reference, including pagination for print journals, is available in PubMed. Our goal is to make mpstruc as accurate and complete as possible. If you find errors or omissions, please send a message to mpstruc emphasizes structures determined by diffraction and cryo-EM methods. NMR structures are also included whenever identified. A comprehensive list of NMR-determined structures has been established by Dror Warschawski and is available from the Atoine Loquet lab.
 

News        Subscribe for rss news updates

  • Members of the Bridge Institute at USC join the mpstruc team: We're pleased to announce that the Ray Stevens and Vadim Cherezov labs will join us in maintaining and improving the mpstruc database. Dr. Gye Won "Gracie" Han will be the voice of the group.
  • Membrane-embedded structures now available!: Mark Sansom's lab at Oxford has created the MemProtMD database of all known transmembrane proteins embedded in lipid membranes, described in Stansfeld et al. (2015) Structure 23:1350-1361. Links to the structures are now included in mpstruc. Click on the icon, and you will be taken to the appropriate entry in MemProtMD.
  • MPtopo XML data representations now available: XML representations are now available for the MPtopo membrane protein topology database.

Latest new protein entered: 11 Aug 2020 at 21:12 PDT.
Last database update: 11 Aug 2020 at 21:18 PDT

New Structures:
Unique proteins in database = 1107
Coördinate files in database = 3129
Published reports of membrane protein structures in database = 2005
A full list of pdb codes currently in the database is available here.

Unique proteins include proteins of same type from different species. For example, photosynthetic reaction centers from R. viridis and R. sphaeroides are considered unique. Structures of mutagenized versions of proteins already in the database are excluded as unique. Proteins that differ only by substrate bound or by physiological state are also excluded. Structures 'obsoleted' by the PDB are not included.

Total number of PDB coördinate files, including those for unique proteins. This number reflects the fact that published reports of structures often include several coördinate files describing, for example, the protein in different crystal forms, or with different bound substrates.


 
A word about the new interface to the protein table.

There are other ways of viewing the data in the mpstruc database besides the hierarchical view presented in the table on this page. The mpstruc database queries page (follow the above link) provides a list of queries on the database, some of which provide tables with sortable columns. Some of the queries may take a few moments. Query results are also available as XML data.

Currently available queries include requesting a list of unique proteins, a list of all published reports, counting unique proteins by year, and counting all published reports by year.

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.

https://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucTblXml
https://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucMonotopicTblXml
https://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucBetaBrlTblXml
https://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucAlphaHlxTblXml

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 uses the following Document Type Definition (DTD):

<!DOCTYPE mpstruc [
  <!ELEMENT mpstruc (caption,groups*)>
  <!ATTLIST mpstruc createdBy CDATA #REQUIRED>
  <!ATTLIST mpstruc maintainedBy CDATA #REQUIRED>
  <!ATTLIST mpstruc copyright CDATA #REQUIRED>
  <!ATTLIST mpstruc url CDATA #REQUIRED>
  <!ATTLIST mpstruc lastNewProteinDate CDATA #REQUIRED>
  <!ATTLIST mpstruc lastDatabaseEditDate CDATA #REQUIRED>
  <!ATTLIST mpstruc timeStamp CDATA #REQUIRED>
  <!ELEMENT caption (#PCDATA)>
  <!ELEMENT groups (group*)>
  <!ELEMENT group (name,proteins,subgroups)>
  <!ELEMENT subgroups (subgroup*)>
  <!ELEMENT subgroup (name,proteins)>
  <!ELEMENT name (#PCDATA)>
  <!ELEMENT proteins (protein*)>
  <!ELEMENT memberProteins (memberProtein*)>
  <!ELEMENT protein (pdbCode,name,species,taxonomicDomain,expressedInSpecies,resolution,description,bibliography,
                     secondaryBibliographies,relatedPdbEntries,memberProteins)>
  <!ELEMENT memberProtein (pdbCode,masterProteinPdbCode,name,species,expressedInSpecies,resolution,
                           description,bibliography,secondaryBibliographies,relatedPdbEntries)>
  <!ELEMENT pdbCode (#PCDATA)>
  <!ELEMENT masterProteinPdbCode (#PCDATA)>
  <!ELEMENT species (#PCDATA)>
  <!ELEMENT taxonomicDomain (#PCDATA)>
  <!ELEMENT expressedInSpecies (#PCDATA)>
  <!ELEMENT resolution (#PCDATA)>
  <!ELEMENT description (#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*)>
  <!ELEMENT relatedPdbEntries (pdbCode*)>
]>

 
Links to the Protein Data Bank Site
Links to the Structural Biology Knowledgebase Site
Membrane Proteins of Known 3D Structure
(Table description)
Protein
PDB Code Links Reference
(links are to PubMed)
MONOTOPIC MEMBRANE PROTEINS
Reviewed by Allen et al. (2018)
TRANSMEMBRANE PROTEINS: BETA-BARREL