4PH3

N-terminal domain of the capsid protein from bovine leukaemia virus (with no beta-hairpin)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.5 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: 10.1126/science.aaa5182
  • Structures With Same Primary Citation

  • 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 repo ...

    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 de Montevideo, Unit of Protein Crystallography, Mataojo 2020, 11400, Montevideo, Uruguay. Institut Pasteur, Department of Structural Biology and Chemistry, 25, Rue du Dr Roux, 75015, Paris, France. pritsch@pasteur.edu.uy alebus@pasteur.edu.uy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BLV capsidA, B129Bovine leukemia virusMutation(s): 0 
Gene Names: gag-pro-pol
Find proteins for L0PI28 (Bovine leukemia virus)
Explore L0PI28 
Go to UniProtKB:  L0PI28
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download CCD File 
A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A,BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
  • Diffraction Data DOI: 10.15785/SBGRID/177 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.613α = 90
b = 66.242β = 90
c = 81.355γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre national de la recherche scientifiqueFranceLaboratoire International Associe LIA 316
Mercosur/FOCEMUruguayCOF 03/11
Mercosur Structural Biology Center CeBEMUruguay--
Agencia Nacional de Investigacion e Innovacion (ANII)Uruguay--

Revision History 

  • 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: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2019-05-15
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2020-01-15
    Changes: Author supporting evidence