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.
The RCSB PDB Poster Prize will also be awarded to recognize a student poster presentation involving macromolecular crystallography.
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.
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: firstname.lastname@example.org.
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.
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.
A "Protein Modification" search has been added to the Advanced Search under the "Sequence Feature" category.
Protein Modifications can be searched by the modification name, keyword, RESID ID, PSI-MOD ID, and the wwPDB Chemical Component ID.
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.
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.
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