What's New

The April 28, 2015 release offers the following features:


3D Structure Visualization

3D Structure Visualization

Support for modern web and mobile browsers

JSmol

JSmol, the JavaScript version of Jmol, is now the default 3D viewer for Structure Summary pages. JSmol supports molecular rendering on modern web browsers and mobile devices. The Jmol Applet is available as an option from the 3D View page, and will continue to work in most browsers (other than Google Chrome)


PV

An experimental version of the JavaScript Protein Viewer PV is offered as an alternative to JSmol. While not as feature-rich as JSmol, it uses WebGL and thus enables hardware-accelerated graphics in modern web and mobile browsers.

PV displays symmetric structures aligned along the symmetry axes. In addition, two of PV's unique features include "out of the browser" views:

  • Detached: launches standalone viewer window that can be resized
  • Full screen: launches a full screen view
4FOH PV view of RuBisCO
PV view of RuBisCO (PDB ID 4F0H) oriented along symmetry axes (red tubes).

Visualizing structures with more than 10,000 residues

Structures containing more than 10,000 residues are a challenge for visualization programs on average personal computers. Currently, JavaScript-based viewers (e.g., JSmol, PV) cannot support large entries and generally the download and rendering process can be slow, causing memory errors and "hanging" applications. To support large structure visualization, this release incorporates:

  • Reduced representation
    • Jmol, Protein Workshop, and Simple Viewer download and use a carbon-alpha and phosphate backbone representation of proteins and nucleic acids, respectively
  • Multi-scale models
    • Protein Workshop and Simple Viewer render proteins as low-resolution surfaces and display nucleic acids as ribbons

Multi-scale rendering of 70S Ribosome from E. coli in Protein Workshop (PDB ID 4V4G)


3D Structure Visualization

Support for Large Structures

PDBx/mmCIF format only

Large structures (containing > 62 chains and/or 99999 ATOM lines) represented as single files have been fully integrated into the main PDB FTP archive in both PDBx/mmCIF and PDBML formats since December 10, 2014.

Search for Large Structures

A new search option has been added to Advanced Search under the category Structure Annotation to find "Large Structures", i.e., structures that do not fit into the legacy PDB file format. This search can be used to find all structures that have PDB format files, or those that do not.



Structure Summary

Previously, large structures were represented in multiple "SPLIT" entries. These "SPLIT" entries have now been superseded by a single entry. This information is listed on the Structure Summary page of these entries.


Top section of Structure Summary page for PDB ID 4WF1, which supersedes and combines 4WAO, 4WAP, 4WAQ, and 4WAR.

Download of Large Structures

In addition, Structure Summary pages of large structures contain a download link to a compressed archive file (tar.gz), which contains a collection of minimal/best effort files in PDB format to support legacy application. Please see this Usage Note for more details. These tar files can also be downloaded in batch, using the Download Tool. Users and developers are urged to adapt to using the PDBx/mmCIF files, rather than the legacy PDB files, to take full advantage of the archive.



Protein Feature View Enhancements

Protein Feature View Enhancements

Proteins from related organisms

The Protein Feature View has a new option to select Protein Feature Views from related organisms with the same gene name.


Protein Feature View for Ribulose bisphosphate carboxylase large chain (P23755). Other organisms with the same gene name can be selected from the menu (the number of available PDB structures is shown in gray circles).

The Action button contains an option to map sequence motifs in the Protein Feature View as shown below.


Active site sequence motif Gx[DN]FxKxDE (Ribulose bisphosphate carboxylase large chain active site) mapped onto protein feature view (red box around mapped region). Note, X matches any amino acid and [DN] matches either D or N. See the Sequence Motif help page for details



Map Genomic Position to Protein Sequence and 3D Structure

Mapping Genomic Position to Protein Sequence and 3D Structure

Mutations in a gene can have profound effects on the function of a protein. A new analysis tool highlights the location of a gene location (i.e., the site of a SNP).


New Analyze option: Map Genomic Position to Protein

Example of SNP in Breast Cancer 1 Gene

A TGT-to-GGT transversion in codon 64 of the BRCA1 gene leads to substitution of glycine for cysteine. This SNP is located on chromosome 17 at genomic coordinate: 43,106,478. The new mapping tool can be used to locate this position on UniProt sequence and 3D structure



The mapping tool displays the position of a SNP on the gene, the UniProt sequence, and 3D structure. By clicking on the green buttons, the consequences of this SNP at the gene, protein, and structure level can be explored.

Position Mapped onto Gene View


The genomic location of this SNP is highlighted by the red bar at position 43,106,478. This gene is read in the reverse direction; therefore, the complement to codon ACA is TGT, which corresponds to a cysteine.

Position Mapped onto Protein Feature View


A red box highlights the Cysteine at UniProt position 64. From this diagram we can see that this position is part of a Zinc finger domain (Pfam track). The structural consequences of a mutation at this position can be analyzed by visualizing this residue in the 3D structure.

Position Mapped onto 3D Structure View


Cysteine 64 is highlighted in CPK style on the PV viewer page. This cysteine forms part of a zinc finger domain and the sulfur of the cysteine (yellow) is coordinated with the zinc ion (purple). Disruption of this interaction has serious functional consequences and has been indicated in breast cancer formation.


Download Tool

Download Tool

The Download Tool can be used to download multiple structure, experimental data (structure factors, NMR restraints), sequence, and ligand files in various file formats in uncompressed and compressed (gzipped) form. Large structures without PDB formatted files can be downloaded as compressed archive files (tar.gz), containing collections of minimal/best effort files in PDB format to support legacy applications.

This tool replaces our earlier Download Applet and requires an up-to-date Java installation (Browser Compatability Check).

The Download Tool is launched as a stand-alone application from the RCSB PDB website using the Java Web Start protocol.

The download page also offers links to download FASTA sequence files and SDF ligand files for the entire archive.


Download Tool Options