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

09/05

wwPDB and the wwPDB Integrative/Hybrid (I/H) Methods Task Force announce 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.



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