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.

Deposit new structures here.

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

Visualization of structures downloaded from PDB-Dev

The multi-scale I/H structures downloaded from PDB-Dev can be vizualized using the ChimeraX software.

Since ChimeraX is under active development, it is recommended to use the Daily Build of ChimeraX for visualization.

Please refer to the Daily Build Notes for information regarding operating systems currently supported by ChimeraX.

The I/H structures can be downloaded as text files (use right click + save as) and opened on ChimeraX using the "format ihm" command line option along with the complete path to the downloaded file:

open path/to/myfile.cif format ihm

Alternately, the following command can be used to directly visualize an entry from PDB-Dev, eg: PDBDEV_00000010.

open 10 from pdbdev

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. Browse all released structures below.

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

Related resource: 10.5281/zenodo.820724

Accession code: PDBDEV_00000001

Download the structure.

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

Related resource: 10.5281/zenodo.583313

Accession code: PDBDEV_00000002

Download the structure.

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

Related resource: 10.5281/zenodo.802915

Accession code: PDBDEV_00000003

Download the structure.

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

Related resource: 10.5281/zenodo.1006721

Accession code: PDBDEV_00000004

Download the structure.

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

Related resource: 10.5281/zenodo.1035833

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

Download the structure.

16Srna_ksga

Structure of 16S rRNA complexed with methyltransferase A small subunit

Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data.

Publication: van Zundert GCP et al., Structure. 2015 May; 23(5):949-60. doi: 10.1016/j.str.2015.03.014

Accession code: PDBDEV_00000014

Download the structure.

NPC

Integrative structure and functional anatomy of a Nuclear Pore Complex

Structure of the 552-protein Nuclear Pore Complex (NPC) from yeast, determined by IMP using spatial restraints derived from cryo-electron tomography and chemical crosslinking experiments.

Publication: Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, et al., Nature. 2018 Mar; 555(7697):475-82

Related resource: 10.5281/zenodo.1194547

Accession codes: PDBDEV_00000010, PDBDEV_00000011, PDBDEV_00000012

Download the structures: NPC single spoke, NPC three spokes, NPC eight spokes

nup133

Integrative structure-function mapping of the nucleoporin Nup133

Integrative structure of the nucleoporin Nup133 obtained using spatial restraints derived from 2DEM class average images and small-angle scattering data.

Publication: Kim SJ et al., Mol Cell Proteomics. 2014 Nov; 13(11):2911-26. doi: 10.1074/mcp.M114.040915

Related resource: 10.5281/zenodo.1209565

Accession code: PDBDEV_00000016

Download the structure.

pom152

Molecular architecture of the major membrane ring component, Pom152, of the yeast nuclear pore complex

Integrative structure of the Pom152 sub-complex obtained using spatial restraints derived from electron microscopy and small-angle scattering data.

Publication: Upla P et al., Structure. 2017 Mar; 25(3):434-45. doi: 10.1016/j.str.2017.01.006

Related resource: 10.5281/zenodo.1231518

Accession code: PDBDEV_00000017

Download the structure.

PDBDEV_00000015

Structure of human mitochondrial iron sulfur cluster core complex (NIAUF)2

Integrative structure of human mitochondrial iron sulfur cluster core complex (NIAUF)2 (NFS1-ISD11-Acp-ISCU-frataxin), obtained by HADDOCK with restraints derived from crosslinking mass spectrometry and NMR experiments.

Publication: Cai K et al., Structure, 2018 in press. doi: 10.1016/j.str.2018.05.017

Accession code: PDBDEV_00000015

Download the structure.

nup82

Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform, Nup82

Integrative structure of the Nup82 sub-complex obtained using spatial restraints derived from chemical crosslinks, electron microscopy and small-angle scattering data.

Publication: Fernandez-Martinez J et al., Cell, 2016 Nov; 167(5):1215-1228. doi: 10.1016/j.cell.2016.10.028

Related resource: 10.5281/zenodo.1256259

Accession code: PDBDEV_00000020

Download the structure.

complement

Structure of complement C3(H2O) revealed by quantitative cross-linking/mass spectrometry and modeling

Integrative structure of complement C3(H2O) obtained using spatial restraints derived from chemical crosslinking and mass spectrometry data.

Publication: Chen ZA et al., Mol Cell Proteomics, 2016 Aug; 15(8):2730-2743. doi: 10.1074/mcp.M115.056473

Related resource: 10.5281/zenodo.1285940

Accession code: PDBDEV_00000021

Download the structure.

Rev7 dimer

Structure of the human Rev7 dimer

Integrative structure of the human Rev7 dimer, modeled by HADDOCK, using the crystal structure of the Rev7-R124A monomer and spatial restraints derived from small-angle scattering and mutagenesis data.

Publication: Rizzo et al., Proc. Natl. Acad. Sci. U. S. A., 2018, in press. doi: 10.1073/pnas.1801149115

Related resource: 10.5281/zenodo.1323686

Accession code: PDBDEV_00000009

Download the structure.

Funding

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

Publications

Vallat B et al., Structure. 2018 Jun; 26(6):894-904. doi: 10.1016/j.str.2018.03.011

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

wwPDB logo