1sva

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1sva, resolution 3.10Å ()
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

SIMIAN VIRUS 40

Publication Abstract from PubMed

BACKGROUND: The structure of simian virus 40 (SV40), previously determined at 3.8 degree resolution, shows how its pentameric VP1 assembly units are tied together by extended C-terminal arms. In order to define more precisely the possible assembly mechanisms, we have refined the structure at 3.1 degree resolution. RESULTS: New data from a high-intensity synchrotron source have been used for phase extension by electron-density averaging and refinement, exploiting only the strict 5-fold non-crystallographic symmetry for the real-space averaging steps. The accurate model enables us to study important structural features of the virus particle in detail. The remarkably invariant core of the VP1 pentamer bears the docking sites for the C-terminal arms from other pentamers. These contacts are the principal way in which pentameric assembly units are linked together in the capsid. Only at the interface between five-coordinated and six-coordinated pentamers do the pentamer cores appear to interact strongly. There are two cation-binding sites per VP1 monomer, seen in a soaking experiment with gadolinium nitrate. These sites are quite close to each other at the interfaces between pentamers. CONCLUSION: We propose that the contact between five-coordinated and six-coordinated pentamers may help to generate a six-pentamer nucleus, with which further pentamers can assemble to generate the complete particle. Calcium ions probably stabilize the structure of the assembled particle, rather than direct its assembly.

The structure of simian virus 40 refined at 3.1 A resolution., Stehle T, Gamblin SJ, Yan Y, Harrison SC, Structure. 1996 Feb 15;4(2):165-82. PMID:8805523

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1sva is a 6 chain structure with sequence from Simian virus 40. The November 2003 RCSB PDB Molecule of the Month feature on Simian Virus 40 by David S. Goodsell is 10.2210/rcsb_pdb/mom_2003_11. Full crystallographic information is available from OCA.

See Also

Reference

  • Stehle T, Gamblin SJ, Yan Y, Harrison SC. The structure of simian virus 40 refined at 3.1 A resolution. Structure. 1996 Feb 15;4(2):165-82. PMID:8805523

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