Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 5040-mer - A5040 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 137.20 kDa 
• Atom Count: 9693 
• Modelled Residue Count: 1239 
• Deposited Residue Count: 1239 
• Unique protein chains: 1

1M4X

PBCV-1 virus capsid, quasi-atomic model

• PDB DOI: 10.2210/pdb1M4X/pdb

• Classification: VIRUS
• Organism(s): Paramecium bursaria Chlorella virus 1
• Mutation(s): No 


• Deposited: 2002-07-05 Released: 2002-12-04 
• Deposition Author(s): Nandhagopal, N., Simpson, A.A., Gurnon, J.R., Yan, X., Baker, T.S., Graves, M.V., Van Etten, J.L., Rossmann, M.G.

---

Experimental Data Snapshot

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

Literature

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

• PubMed: 12411581 
• DOI: 10.1073/pnas.232580699
• Primary Citation of Related Structures:  
  1M4X


• 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PBCV-1 virus capsid	A, B, C	413	Paramecium bursaria Chlorella virus 1	Mutation(s): 0  Gene Names: A430L
UniProt
Find proteins for P30328 (Paramecium bursaria Chlorella virus 1) Explore P30328  Go to UniProtKB:  P30328

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-07-05 
• Released Date: 2002-12-04 
Deposition Author(s): Nandhagopal, N., Simpson, A.A., Gurnon, J.R., Yan, X., Baker, T.S., Graves, M.V., Van Etten, J.L., Rossmann, M.G.

Revision History  

• 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