Recent News Articles

Meet the RCSB PDB at ACA

07/19

RCSB PDB News Image

From July 22-26, RCSB PDB will be at the 2016 Meeting of the American Crystallographic Association (ACA) in Denver, CO.

Visit exhibition booth #46 to pick up new materials and meet with RCSB PDB Director Stephen K. Burley, Director Emerita and Associate Director Helen Berman, Deputy Director Christine Zardecki, and Scientific Support & Customer Service Lead Rachel Kramer Green.

Presentations include:

  • Saturday, Poster 85: A Data Dictionary for Archiving Integrative/Hybrid Models. Helen Berman will describe the creation of 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
  • Sunday, Poster 139: PDB-101: Educational Portal for Molecular Explorations of Biology and Medicine from the RCSB Protein Data Bank. The features of the educational portal at pdb101.rcsb.org will be highlighted by Christine Zardecki. PDB-101 hosts the Geis Digital Archive, which integrates many of Irving Geis’ iconic images of structures with corresponding PDB data.
  • Monday, Poster 111: RCSB Protein Data Bank: Views of Structural Biology for Basic and Applied Research. Stephen Burley and Rachel Kramer Green will discuss the tools and resources available at rcsb.org for searching, visualizing, and analyzing PDB data.

The RCSB PDB Poster Prize will also be awarded to recognize a student poster presentation involving macromolecular crystallography.



Summer Newsletter Published

07/12

The Summer 2016 issue of the RCSB PDB Newsletter is now online. Meet our summer interns, watch the 2016 Video Challenge award winners, explore protein modifications in the PDB, and more.

In the Education Corner, Krystle J. McLaughlin describes Lysozyme, Models and the PDB: Helping Undergraduates Explore Structure.


RCSB PDB's Newsletter is published and archived online.



Announcement: Map Volume Deposition to EMDB Will Be Mandatory for PDB Depositions of 3DEM models Starting September 6th, 2016

07/06

Effective September 6th, 2016, deposition to the PDB of atomic models determined by 3D Electron cryo-Microscopy (3DEM) will require prior or simultaneous deposition of the associated 3DEM volume maps to EMDB.

Maps and models can be deposited at a member site of the Worldwide Protein Data Bank (wwpdb.org) using the joint PDB, EMDB and BMRB deposition tool made available by RCSB PDB (http://deposit.wwpdb.org), PDBe (https://deposit-pdbe.wwpdb.org), and PDBj (http://deposit-pdbj.wwpdb.org).

Data can be released following the authors' release instructions, once they have been processed and approved. wwPDB and EMDB policies both allow for a maximum hold period of one year for model and associated map depositions. Note that (starting September 6th, 2016) for joint PDB/EMDB depositions, the hold period will be the same for the map(s) and the model(s).

This policy change aligns the deposition requirements for 3DEM models with those for structures determined by other techniques, for which deposition of experimental data has been mandatory since 2008. The policy change was developed on the basis of input from the PDB and EMDB user communities and has been unanimously endorsed by the wwPDB Advisory Committee.

Questions regarding depositions should be sent to: deposit-help@mail.wwpdb.org.



Biological Assembly files for large structures

07/05

Biological assembly files for large structures are now available for download from the Structure Summary page in the PDBx/mmCIF format. These files are also available on the FTP site (ftp://ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/). The PDBx/mmCIF format has no restrictions on the number of atoms and chains and can hold biological assemblies of any size.
The biological assembly is the macromolecular assembly that has either been shown to be or is believed to be the functional form of the molecule. For more information, see PDB-101’s biological assembly tutorial.

RCSB PDB News Image"Download files" menu for a large structure PDB ID 5FDV. In this case, the asymmetric unit contains two copies of the ribosome. They are represented as two biological assemblies files: 5fdv-assembly1.cif.gz and 5fdv-assembly2.cif.gz.



2016 Index