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Newsletter | Fall 2017 ⋅ Number 75

Data Deposition and Annotation

Deposition Statistics

In the third quarter of 2017, 3067 experimentally-determined structures were deposited to the PDB archive for a total of 10176 entries deposited in the year.

Of the structures deposited in 2017 so far, 77.3% were deposited with a release status of hold until publication; 18.2% were released as soon as annotation of the entry was complete; and 4.4% were held until a particular date.

92.1% of these entries were determined by X-ray crystallographic methods; 3.2% were determined by NMR methods.

During the same time quarter, 2489 structures were released in the PDB.

Better Management of PDB Archive with File Versioning and Revision History

As announced on May 17, 2017, wwPDB will introduce a file versioning system on October 3 to retain depositor-initiated updates of previously released coordinate entries. A new FTP repository will host versioned files. Versions will be separated into major and minor updates. Updates to atomic coordinates, polymer sequence or chemical description in a PDB coordinate file will trigger a major version increment. Other changes will be classified as minor. All latest major versions of each PDB structure will be retained in the new FTP archive.

wwPDB will deliver versioned files in two phases:

  • Phase 1 (October 2017), we will release the new versioned FTP archive at ftp://ftp-version.wwpdb.org for structural model files in PDBx/mmCIF and PDBML formats.
  • Phase 2 will be released in 2018 and will support depositor-initiated updates of coordinates in PDBx/mmCIF and PDBML formats.

Visit wwPDB.org for more information.

PDB-Dev: A Prototype System for Integrative/Hybrid Structural Models

Integrative model of the Nup84 sub-complex from the nuclear pore complex of budding yeast. Explore at pdb-dev.wwpdb.org

wwPDB and the wwPDB Integrative/Hybrid (I/H) Methods Task Force have announced the public release of a prototype system for depositing I/H structural models, PDB-Development (or “PDB-Dev”) at pdb-dev.wwpdb.org.

Structural characterization of complex macromolecular assemblies is increasingly being carried out using I/H methods. Traditional structure determination methods such as X-ray crystallography and NMR spectroscopy are generally insufficient for tackling such complex assemblies. Recently, methods have been developed that combine spatial restraints derived from a variety of complementary experimental techniques, including cryo-electron microscopy, small angle scattering, chemical crosslinking, mass spectrometry and other proteomics and bioinformatics tools.

PDB-Dev was established to make I/H models available to the broader biological research community. It incorporates recommendations published by the wwPDB I/H Methods Task Force (1). PDB-Dev was built based on a data dictionary that captures the details of I/H models including a variety of experimentally-derived spatial restraints and the modeling of multi-scale, multi-state, time-ordered ensembles. The dictionary is an extension of the PDBx/mmCIF dictionary used by the wwPDB to archive macromolecular structures.

Currently, three test cases covering a variety of features of the Integrative Modeling Platform software (IMP, 2) have been deposited to PDB-Dev, including the 7-piece Nup84 sub-complex of the nuclear pore complex from yeast (3), the yeast exosome complex (4), and the yeast mediator complex (5).

PDB-Dev has been announced in Structure:

PDB-Dev: A Prototype System for Depositing Integrative/Hybrid Structural Models Stephen K. Burley, Genji Kurisu, John L. Markley, Haruki Nakamura, Sameer Velankar, Helen M. Berman, Andrej Sali, Torsten Schwede, Jill Trewhella Structure 2017 25: 1317-1318 doi: 10.1016/j.str.2017.08.001

wwPDB Partnership is committed to encouraging development of methods for archiving and validating I/HM structural data, and has published a policy governing I/HM depositions and the PDB archive.

Creation of PDB-Dev and the I/H methods data dictionary were supported by NSF EAGER award number 1519158.

References

  1. Sali, A., Berman, H.M., Schwede, T., Trewhella, J., Kleywegt, G., Burley, S.K., Markley, J., Nakamura, H., Adams, P., Bonvin, A.M., Chiu, W., Peraro, M.D., Di Maio, F., Ferrin, T.E., Grunewald, K., Gutmanas, A., Henderson, R., Hummer, G., Iwasaki, K., Johnson, G., Lawson, C.L., Meiler, J., Marti-Renom, M.A., Montelione, G.T., Nilges, M., Nussinov, R., Patwardhan, A., Rappsilber, J., Read, R.J., Saibil, H., Schroder, G.F., Schwieters, C.D., Seidel, C.A., Svergun, D., Topf, M., Ulrich, E.L., Velankar, S., and Westbrook, J.D., Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure, 2015. 23(7): p. 1156-67. doi:10.1016/j.str.2015.05.013.
  2. Russel, D., Lasker, K., Webb, B., Velazquez-Muriel, J., Tjioe, E., Schneidman-Duhovny, D., Peterson, B., and Sali, A., Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol, 2012. 10(1): p. e1001244. doi:10.1371/journal.pbio.1001244.
  3. Shi, Y., Fernandez-Martinez, J., Tjioe, E., Pellarin, R., Kim, S.J., Williams, R., Schneidman-Duhovny, D., Sali, A., Rout, M.P., and Chait, B.T., Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol Cell Proteomics, 2014. 13(11): p. 2927-43. doi:10.1074/mcp.M114.041673.
  4. Shi, Y., Pellarin, R., Fridy, P.C., Fernandez-Martinez, J., Thompson, M.K., Li, Y., Wang, Q.J., Sali, A., Rout, M.P., and Chait, B.T., A strategy for dissecting the architectures of native macromolecular assemblies. Nat Methods, 2015. 12(12): p. 1135-8. doi:10.1038/nmeth.3617.
  5. Robinson, P.J., Trnka, M.J., Pellarin, R., Greenberg, C.H., Bushnell, D.A., Davis, R., Burlingame, A.L., Sali, A., and Kornberg, R.D., Molecular architecture of the yeast Mediator complex. Elife, 2015. 4. doi:10.7554/eLife.08719.