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.

Browse PDB-Dev

The PDB-Dev prototype system currently consists of integrative/hybrid models that follow the specifications defined in the I/H methods dictionary, which is a modular extension of the PDBx/mmCIF dictionary. These include atomistic models as well as multi-scale models consisting 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.

Accession code: PDBDEV_00000001

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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.

Accession code: PDBDEV_00000002

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Mediator

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.

Accession code: PDBDEV_00000003

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Diubiquitin

Structure of K63-linked Diubiquitin

Characterization of K63-linked diubiquitin using chemical crosslinking coupled with mass spectrometry (CXMS), small-angle X-ray scattering (SAXS), and smFRET techniques.

Publication: Liu Z et al., Biochemistry. 2017 Oct. doi: 10.1021/acs.biochem.7b00817.

Accession code: PDBDEV_00000004

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HSA_B

Serum Albumin Domain Structures

Structures of human serum albumin domains, obtained from purified samples in their native enviroment, are elucidated using chemical crosslinking coupled with mass spectrometry (CXMS) experiments and computational biology algorithms.

Publication: Belsom A et al., Mol Cell Proteomics. 2016 Mar; 15(3):1105-16. doi: 10.1074/mcp.M115.048504.

Accession codes: PDBDEV_00000005, PDBDEV_00000006, PDBDEV_00000007

Download the structures: HSA Domain A, HSA Domain B, HSA Domain C

fly_genome

Fly Genome Structure: Chromosome 2L

Modeling of genomes and genomic domains using restraints derived from Chromosome Conformation Capture (3C) experiments.

Publication: Trussart M et al., Nucleic Acids Res. 2015 Apr; 43(7):3465-77. doi: 10.1093/nar/gkv221.

Accession code: PDBDEV_00000008

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Funding

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

Publication

The announcement of PDB-Dev has been published in Structure:

Burley et al., Structure. 2017 Sep; 25(9):1317-1318. doi: 10.1016/j.str.2017.08.001.

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