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.



Explore Protein Modifications

07/05

Proteins are modified at different stages of protein synthesis, including pre-translational (i.e., N-formylation), co-translational, and post-translational modifications.

Protein Modifications in the PDB have been mapped to the RESID database of Protein Modifications (J.S. Garavelli, Nucl. Acids Res. (2003), 31, 499-501) and the associated Protein Modifications Ontology PSI-MOD (L. Montecchi-Palazzi, et al., Nat. Biotech (2008), 26, 864-866).

Below, we describe how to browse, search, and visualize protein modifications.

Tree Browser

Protein modifications can be browsed by two PSI-Mod Ontologies, categorized by either the amino acid involved in the modification or by the chemical process involved in the formation.

The Protein Modification Browser can be accessed by clicking on the "Browse by Annotations" link under the text search box on the home page. The tree browser hierarchy can be expanded by clicking on the triangles or by typing in text in the autocomplete search box. For each branch of the tree hierarchy, the number of PDB structures that contain the modification is displayed and is linked to the search results page.

RCSB PDB News ImageProtein Modification Tree Browser

Advanced Search

A "Protein Modification" search has been added to the Advanced Search under the "Sequence Feature" category.

RCSB PDB News ImageAdvanced Search menu

Protein Modifications can be searched by the modification name, keyword, RESID ID, PSI-MOD ID, and the wwPDB Chemical Component ID.

RCSB PDB News ImageProtein Modification Advanced Search Options

Protein Modification Track on Sequence tab

The Sequence tab option on Structure Summary pages visually maps an entry’s sequence with structural annotations. A new annotation protein modification is now available. The type of modification and links to the RESID database and the PSI-MOD ontology are given in the text box on the left. The color code in the annotations box is used to highlight the modification on the sequence display. In addition, a legend on the bottom explains the symbols and colors used for each modification.

RCSB PDB News ImageProtein Modification Track on Sequence tab (Example PDB ID 5EVB shows a hexacoordinated zinc ion and an L-cystine cross-link). The shape of the symbol indicates the number of residues involved in a cross-link (e.g., vertical bar: between two residues, hexagon: hexacoordinated group). The lines link the cross-linked residues.

Visualize Protein Modifications in 3D

The JSmol 3D view page, available from an entry’s Structure Summary page, offers special tools for viewing ligand interactions and protein domains. The ability to view specific protein modifications in 3D has been added to these options. To access this view, scroll down to the bottom of the 3D View page and select the “Modification” tab. Selecting a feature listed in the “type” column will highlight the modification in the 3D viewer above.

RCSB PDB News ImageJSmol visualization of protein modifications (Example PDB ID 5EVB with L-cystine modification selected in the Modification tab of the JSmol page).


2016 Index