PBCV-1 virus capsid, quasi-atomic model

Experimental Data Snapshot

  • Resolution: 28.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


The Structure and Evolution of the Major Capsid Protein of a Large, Lipid containing, DNA virus.

Nandhagopal, N.Simpson, A.Gurnon, J.R.Yan, X.Baker, T.S.Graves, M.V.Van Etten, J.L.Rossmann, M.G.

(2002) Proc Natl Acad Sci U S A 99: 14758-14763

  • DOI: https://doi.org/10.1073/pnas.232580699
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-A resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel beta-barrel, "jelly-roll" domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-A diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus.

  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PBCV-1 virus capsid
A, B, C
413Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Find proteins for P30328 (Paramecium bursaria Chlorella virus 1)
Explore P30328 
Go to UniProtKB:  P30328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30328
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 28.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-11-06
    Changes: Data collection, Database references, Other
  • Version 1.5: 2019-11-13
    Changes: Data collection, Other
  • Version 1.6: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description