2V4X

Crystal Structure of Jaagsiekte Sheep Retrovirus Capsid N-terminal domain

• PDB DOI: https://doi.org/10.2210/pdb2V4X/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Jaagsiekte sheep retrovirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-09-30 Released: 2008-11-25 
• Deposition Author(s): Mortuza, G.B., Goldstone, D.C., Pashley, C., Haire, L.F., Palmarini, M., Taylor, W.R., Stoye, J.P., Taylor, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.185 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 

Literature

Structure of the Capsid Amino-Terminal Domain from the Betaretrovirus, Jaagsiekte Sheep Retrovirus.

Mortuza, G.B., Goldstone, D.C., Pashley, C., Haire, L.F., Palmarini, M., Taylor, W.R., Stoye, J.P., Taylor, I.A.

(2009) J Mol Biol 386: 1179

• PubMed: 19007792 
• DOI: https://doi.org/10.1016/j.jmb.2008.10.066
• Primary Citation of Related Structures:  
  2V4X


• PubMed Abstract: 
  

  Jaagsiekte sheep retrovirus is a betaretrovirus and the causative agent of pulmonary adenocarcinoma, a transmissible lung tumour of sheep. Here we report the crystal structure of the capsid amino-terminal domain and examine the self-association properties of Jaagsiekte sheep retrovirus capsid. We find that the structure is remarkably similar to the amino-terminal domain of the alpharetrovirus, avian leukosis virus, revealing a previously undetected evolutionary similarity. Examination of capsid self-association suggests a mode of assembly not driven by the strong capsid carboxy-terminal domain interactions that characterise capsid assembly in the lentiviruses. Based on these data, we propose this structure provides a model for the capsid of betaretroviruses including the HML-2 family of endogenous human betaretroviruses.

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Organizational Affiliation: 

Division of Molecular Structure, National Institute for Medical Research, the Ridgeway, Mill Hill, London NW7 1AA, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 16.12 kDa 
• Atom Count: 1,289 
• Modelled Residue Count: 131 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAPSID PROTEIN P27	A	140	Jaagsiekte sheep retrovirus	Mutation(s): 0
UniProt
Find proteins for P31622 (Sheep pulmonary adenomatosis virus) Explore P31622  Go to UniProtKB:  P31622

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.185 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.595	α = 90
b = 57.826	β = 109.17
c = 40.927	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Mortuza, G.B., Goldstone, D.C., Pashley, C., Haire, L.F., Palmarini, M., Taylor, W.R., Stoye, J.P., Taylor, I.A.

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance