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Review
. 2006 Jan;63(1):36-51.
doi: 10.1007/s00018-005-5350-6.

The Membrane Protein Data Bank

P Raman  1 , V Cherezov, M Caffrey
Affiliations
Review

The Membrane Protein Data Bank

P Raman et al. Cell Mol Life Sci. 2006 Jan.

Abstract

The Membrane Protein Data Bank (MPDB) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. Data originates from the Protein Data Bank and other databases, and from the literature. Structures are based on X-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. The MPDB is searchable online by protein characteristic, structure determination method, crystallization technique, detergent, temperature, pH, author, etc. Record entries are hyperlinked to the PDB and Pfam for viewing sequence, three-dimensional structure and domain architecture, and for downloading coordinates. Links to PubMed are also provided. The MPDB is updated weekly in parallel with the Protein Data Bank. Statistical analysis of MPDB records can be performed and viewed online. A summary of the statistics as applied to entries in the MPDB is presented. The data suggest conditions appropriate for crystallization trials with novel membrane proteins.

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Figures

Figure 1
Figure 1
Cartoon representation of the membrane topologies featured in the MPDB. Thin horizontal lines demark the membrane in and on which the protein (bold lines) sits. The simplest polytopic protein, with just two membrane crossings, is shown.
Figure 2
Figure 2
The MPDB Main Page.
Figure 3
Figure 3
An MPDB record.
Figure 4
Figure 4
A typical MPDB summary table.
Figure 5
Figure 5
A screen shot of a default statistical analysis performed on all MPDB records versus expression system.
Figure 6
Figure 6
pH dependence of the number of records in the MPDB across all structure determination methods.
Figure 7
Figure 7
Dependence of the cumulative MPDB record count on the year of primary citation publication. The analysis was performed on all records in the MPDB (blue-green), on XRD records across all crystallization methods (red), and on XRD records in the lipidic cubic phase method subset (black). An exponential best fit to data in blue-green in the period 1982–2004 is shown as a solid black line. The equation for the line takes the form Y = A e−B (X − 1982) where Y is cumulative count, X is year, A is 2.0 and B is 0.251. Note that the data for 2005 only include records for the first 6 months of that year and are identified by open symbols.
See this image and copyright information in PMC

References

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