Welcome to PDB-Dev

PDB-Dev is a prototype deposition and archiving system for structural models obtained through integrative/hybrid (I/H) methods. Structural characterization of many complex macromolecular assemblies are increasingly carried out using I/H methods, where a combination of complementary experimental and computational techniques are used to determine the structure. The structural models obtained through I/H methods are collected, archived and disseminated to the public through PDB-Dev.

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More information of how to deposit structures can be found in the FAQ section.

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The PDB-Dev prototype system currently consists of integrative/hybrid models built using the Integrative Modeling Platform (IMP). The models follow the specifications defined in the I/H methods dictionary, which is a modular extension of the PDBx/mmCIF dictionary. These are multi-scale models that consist of different coarse-grained representations.

Nup 84

Structure of the Nup84 sub-complex of the Nuclear Pore Complex

The Nup84 structure from budding yeast has been determined by IMP using spatial restraints derived from two-dimensional Electron Microscopy (2DEM) and chemical crosslinking followed by mass spectrometry (CX-MS) experiments.

Publication: Shi et al., Mol Cell Proteomics. 2014 Nov;13(11):2927-43. doi: 10.1074/mcp.M114.041673.

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Exosome

Structure of the Exosome Complex

The structure of the Exosome complex has been determined by IMP using spatial restraints derived from chemical crosslinking data followed by mass spectrometry (CX-MS) experiments.

Publication: Shi et al., Nat Methods. 2015 Dec; 12(12):1135-1138. doi: 10.1038/nmeth.3617.

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Exosome

Structure of the Mediator Complex

The structure of the Mediator complex has been determined by IMP using spatial restraints derived from three-dimensional Electron Microscopy (3DEM) and chemical crosslinking data followed by mass spectrometry (CX-MS) experiments.

Publication: Robinson et al., Elife. 2015 Sep; 4. pii: e08719. doi: 10.7554/eLife.08719.

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Funding

The development of the PDB-Dev prototype system has been funded by an NSF EAGER grant (DBI-1519158).

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