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WHAT'S NEW

The August 13, 2014 release offers the following new features:

New Top Bar Menu

Providing More Space to Users

The new navigation menu at the top of the website replaces the left-hand menu to provide more space for search results. The RCSB PDB will continue to improve the usability of rcsb.org.

RCSB PDB Top Bar Navigation

Gene View

Gene Structure and Mapping to PDB Entries for Human Genes

A new Gene View illustrates the correspondences between the human genome and 3D structure. All human genes have been mapped to representative PDB protein chains (chosen from sequence clusters at 40% sequence identity) to show which regions of a gene are available in PDB coordinates.

This feature requires an up-to-date web browser.

Gene View : Gene Structure and Mapping to PDB Entries for Human Genes

Gene View for gene HBA1 : Hemoglobin alpha protein representative chains 2W72.A and 1C7C.A (blue) mapped to exons of HBA1 gene (orange)

The graphical view is built on top of the BioDalliance genome browser. Users can use the mouse to move through the region around a human gene as shown in the Gene View.

Gene View displays information in several horizontal rows called tracks, which can be reordered by dragging the title box. The view can be zoomed in or out.

  • The Genome track displays the position of the region of the genome and the nucleotide (when zoomed out as a letter code, when zoomed in as a color-coded region (Guanine: black, Adenine: green, Cytosine: blue, Thymine: red).
  • The PDB track shows the region of the gene with available PDB protein chains. Clicking on the region displays more information about the mapped protein.
  • The Genes track displays the annotated gene, as provided by the Gencode project. White boxes represent UTRs (untranslated regions) and orange boxes represent protein coding regions. Black lines connecting boxes represent introns (regions that get removed during mRNA splicing).
  • The Repeats track shows regions that have been annotated to contain various repeats. Data provided by UCSC Genome Browser.
  • The Conservation track shows PhastCons conservation scores derived from multiple alignments of 45 vertebrate genomes to the human genome. Data provided by UCSC Genome Browser.

Gene View can be launched from a Structure Summary page for a human protein under "Molecular Description":

2W72 Structure Summary

Molecular description section from the 2W72 Structure Summary page with links to Gene View for genes HBA1 and HBA2

The Gene View is also accessible from the top bar search box by selecting a matched gene symbol from the autocomplete suggestions:

Gene View in Search Bar

Link to Gene View for gene HBA1 using the autocomplete search suggestions (Note: Protein Feature View is also accessible using the gene symbol: see next section).

Protein Feature View

Enhanced with New Information

The Protein Feature View has been redesigned to improve readability and to add descriptions of protein function, subunit structure, domains from UniProt, and an Exon Structure track from the gene mapping described above.

Protein Feature View can be launched from the "Molecular Description" section of a Structure Summary page as well as by searching for a UniProt ID or Gene Symbol.

P69905 Human

Protein Feature View for UniProt ID P69905 showing the new Exon Structure track

Ramachandran Plots

Enhancing Protein Structure Validation

Structure Summary pages for X-ray crystal structures now provide access to a PDF version of the the full PDB Validation Report for the entry in addition to the display of the report's "slider" graphic. These reports, which provide an assessment of the quality of a structure and highlight specific concerns, were created using the recommendations of the wwPDB X-ray Validation Task Force.

Also, links to new Ramachandran plots created by MolProbity (version 4.02b) have been added to Structure Summary pages. The plots can be downloaded as a PDF file Ramachandran plots provide an independent method to evaluate the conformational quality of protein structures.

Ramachandran Plot

Reference data for six classes of Ramachandran plots. Conformations outside the outer contour line are considered outliers (Source: J. Richardson, et al.)

Access to these views was suggested by the wwPDB X-ray Validation Task Force. The Ramachandran plots provide a visual representation of outliers tabulated in the Validation Report PDF.

Structure Validation

Links to the full validation report and Ramachandran Plots from the Structure Summary page for entry 3WQ8

Previously, Ramachandran plots were located on the Geometry tab, which has been retired. Additional validation data and statistics are available from the Structure Summary Links tab, including reports by WHAT_CHECK and PROCHECK.

Average Temperature (B) Factor

New Field in Tabular Reports

Refinement Details

The average temperature (B) factor has been added to the Refinement Details section of the tabular report creation options.