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