4PH2

mature N-terminal domain of capsid protein from bovine leukemia virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

STRUCTURAL VIROLOGY. Conformational plasticity of a native retroviral capsid revealed by x-ray crystallography.

Obal, G.Trajtenberg, F.Carrion, F.Tome, L.Larrieux, N.Zhang, X.Pritsch, O.Buschiazzo, A.

(2015) Science 349: 95-98

  • DOI: https://doi.org/10.1126/science.aaa5182
  • Primary Citation of Related Structures:  
    4PH0, 4PH1, 4PH2, 4PH3

  • PubMed Abstract: 

    Retroviruses depend on self-assembly of their capsid proteins (core particle) to yield infectious mature virions. Despite the essential role of the retroviral core, its high polymorphism has hindered high-resolution structural analyses. Here, we report the x-ray structure of the native capsid (CA) protein from bovine leukemia virus. CA is organized as hexamers that deviate substantially from sixfold symmetry, yet adjust to make two-dimensional pseudohexagonal arrays that mimic mature retroviral cores. Intra- and interhexameric quasi-equivalent contacts are uncovered, with flexible trimeric lateral contacts among hexamers, yet preserving very similar dimeric interfaces making the lattice. The conformation of each capsid subunit in the hexamer is therefore dictated by long-range interactions, revealing how the hexamers can also assemble into closed core particles, a relevant feature of retrovirus biology.


  • Organizational Affiliation

    Institut Pasteur, Unité de Virologie Structurale, Département de Virologie and CNRS Unité Mixte de Recherche 3569, 28, Rue du Docteur Roux, 75015, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BLV capsid - N-terminal domain
A, B
134Bovine leukemia virusMutation(s): 0 
Gene Names: gag-pro-pol
UniProt
Find proteins for L0PI28 (Bovine leukemia virus)
Explore L0PI28 
Go to UniProtKB:  L0PI28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0PI28
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.67α = 90
b = 56.04β = 90
c = 103.07γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references
  • Version 1.2: 2015-07-15
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Advisory, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description