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wwPDB Deposition & Annotation System Now Available for NMR and 3DEM Structures

01/10 wwPDB News

The wwPDB partners are pleased to announce the launch of a new Deposition & Annotation system that supports structures determined using 3DEM, NMR, and X-ray, neutron and electron crystallography. New entries from all methods can be submitted online (RCSB PDB | PDBe | PDBj).

This new system interoperates with EMDB and BMRB to enable joint depositions of both atomic coordinates (PDB) and EM electron-density maps (EMDB) or NMR experimental data (BMRB). PDB, EMDB and BMRB accession codes will be issued as appropriate immediately after a structure has been deposited.

A brief tutorial is available at http://www.wwpdb.org/deposition/tutorial.

In January 2014, the wwPDB launched the Deposition & Annotation system for structures determined using X-ray crystallography in the first phase of our roll-out of a single global system for deposition and annotation of structural data. Using this system, more than 12,000 X-ray structures have been deposited and annotated, and more than 6,800 entries released in the PDB archive.

New or enhanced features of the global combined X-ray/3DEM/NMR wwPDB Deposition & Annotation system include generation and review of validation reports that follow wwPDB Task Force recommendations,1,2,3 improved capture and review of ligand information, replacement of atomic coordinate and/or experimental data files both pre- and post-submission, and improved communication between depositors and wwPDB curators.

In addition to the new system, depositors will continue to have the option of using one of the legacy deposition tools (EMDep, ADIT-NMR, AutoDep) to start a new deposition for at least the first half of 2016.

Once the new system is deemed stable, the legacy deposition tools will be phased out with sufficient time allowed for completion of in-progress sessions. This process mirrors the one used in early 2015 for successful shutdown of the legacy ADIT system supporting deposition of X-ray structures.

  1. A New Generation of Crystallographic Validation Tools for the Protein Data Bank, Randy J. Read, Paul D. Adams, W. Bryan Arendall III, Axel T. Brunger, Paul Emsley, Robbie P. Joosten, Gerard J. Kleywegt, Eugene B. Krissinel, Thomas Lütteke, Zbyszek Otwinowski, Anastassis Perrakis, Jane S. Richardson, William H. Sheffler, Janet L. Smith, Ian J. Tickle, Gert Vriend and Peter H. Zwart. (2011) Structure 19: 1395-1412 doi: 10.1016/j.str.2011.08.006
  2. Outcome of the First Electron Microscopy Validation Task Force Meeting, Richard Henderson, Andrej Sali, Matthew L. Baker, Bridget Carragher, Batsal Devkota, Kenneth H. Downing, Edward H. Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff, Wen Jiang, Steven J. Ludtke, Ohad Medalia, Pawel A. Penczek, Peter B. Rosenthal, Michael G. Rossmann, Michael F. Schmid, Gunnar F. Schröder, Alasdair C. Steven, David L. Stokes, John D. Westbrook, Willy Wriggers, Huanwang Yang, Jasmine Young, Helen M. Berman, Wah Chiu, Gerard J. Kleywegt, and Catherine L. Lawson. (2012) Structure 20: 205-214 doi:10.1016/j.str.2011.12.014
  3. Recommendations of the wwPDB NMR Validation Task Force, Gaetano T. Montelione, Michael Nilges, Ad Bax, Peter Güntert, Torsten Herrmann, Jane S. Richardson, Charles D. Schwieters, Wim F. Vranken, Geerten W. Vuister, David S. Wishart, Helen M. Berman, Gerard J. Kleywegt, and John L. Markley. (2013) Structure 21: 1563-1570 doi:10.1016/j.str.2013.07.021

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