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New Images for Transmembrane Proteins

10/11

New images for transmembrane proteins

RCSB PDB provides additional annotations and query options for transmembrane proteins.

New high resolution images for transmembrane proteins were created using information from the Orientations of Proteins in Membranes (OPM) database.

RCSB PDB News ImageNew transmembrane view for the pentameric ligand gated ion channel GLIC (PDB ID: 2xq7)

Molecular graphics and analyses performed with UCSF ChimeraX, developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).

Data source: Orientations of Proteins in Membranes (OPM) database

Data about the orientation of transmembrane proteins are provided by the Orientations of Proteins in Membranes (OPM) database, when available. OPM is updated less frequently than the PDB, so not all transmembrane proteins will have these images.

Types of images

These transmembrane images (when available) are the first image shown on the Structure Summary page. Membranes are represented as red (outside) and blue (inside) planes. Images for the biological assembly and asymmetric unit are also available.

RCSB PDB News ImageThe 'cartoon' style is the default view for the new transmembrane images.
RCSB PDB News ImageThe 'surface' rendering provides an indication of the volume of the protein.
RCSB PDB News ImageThe 'flat' display provides an abstract representation that in some cases can highlight symmetries.
RCSB PDB News ImageColoring by 'lipophilicity' indicates the ability of atoms to dissolve in the lipid bi-layer.

References

  • Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: Orientations of Proteins in Membranes database. Bioinformatics 22, 623-625 pubmed
  • OPM homepage
  • UCSF ChimeraX


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