RCSB PDB Newsletter #20: Biological Unit Tutorial Now Available from the RCSB PDB

No. 20
Winter 2004


Message from the RCSB PDB

Announcing the Worldwide Protein Data Bank

Downloadable PDB_EXTRACT Makes Deposition Easier

Biological Unit Tutorial Now Available from the RCSB PDB

Ligand Depot--a Small Molecule Information Resource

PDB Focus: Deposition and Release Policies

PDB Deposition Statistics

Lucene Keyword Search Released on the RCSB PDB Web Site

PDB Focus: Redundancy Reduction Cluster Data Available on the PDB FTP Site

PDB Focus: Searching for Experimental Data Files

Updates of mmCIF Files on the RCSB PDB FTP Site

RCSB PDB Web Site Statistics

NIGMS News: PSI-2 and Structural Biology Roadmap RFA

RCSB PDB Article Published in Nucleic Acids Research

New Update Release of CD-ROM Sets

PDB Molecules of the Quarter: Trypsin, Simian Virus 40, and Catabolite Activator Protein

PDB Community Focus: Edward N. Baker

PDB Education Corner by Katherine Kantardjieff

Related Links: FTP Resources

RCSB PDB Job Listings

RCSB PDB Members & Statement of Support

Questions? info@rcsb.org

© 2004 RCSB PDB


Biological Unit Tutorial Now Available from the RCSB PDB

An introduction to biological units in the PDB archive is now accessible at www.rcsb.org/pdb/biounit_tutorial.html. This useful guide offers detailed explanations and examples of the asymmetric unit and the biological molecule, indicates where information about the biological unit can be found in PDB and mmCIF coordinate files, and describes how the biological unit files in the PDB have been derived.

The RCSB PDB offers images and coordinates for the complete biological unit of crystallographic entries in the archive. The biological molecule, or biological unit, is the macromolecule that has been shown to be or is believed to be functional. When crystallographic structures are deposited into the PDB, the primary coordinate file generally contains one asymmetric unit--the smallest portion of a crystal structure to which crystallographic symmetry can be applied to generate one unit cell. In some cases, the asymmetric unit differs from the biologically active molecule. The RCSB PDB provides data on biological units to further an understanding of molecular function.

The biological unit tutorial is also linked from the View Structure and Download/Display File sections of the Structure Explorer page, as well as under PDB WWW User Guides. For more information, please send inquiries to info@rcsb.org.

In the structure of the host range-controlling region of feline parvovirus in entry 1p5y, non-crystallographic symmetry is used to create the icosohedral viral capsid from sixty copies of the one protein chain contained in the coordinate file. The viral capsid is both the asymmetric unit and the biological unit.
PDB ID: 1p5y
L. Govindasamy, K. Hueffer, C.R. Parrish, M. Agbandje-McKenna (2003): Structures of host range-controlling regions of the capsids of canine and feline parvoviruses and mutants. J. Virol. 77, p. 12211.