Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 16.20 kDa 
• Atom Count: 1130 
• Residue Count: 142 
• Unique protein chains: 1

4HTW

SIVmac239 capsid N-terminal domain

• DOI: 10.2210/pdb4HTW/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Simian immunodeficiency virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-02 Released: 2013-05-22 
• Deposition Author(s): Schmidt, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.293 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 

Literature

Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5alpha Specificity.

McCarthy, K.R., Schmidt, A.G., Kirmaier, A., Wyand, A.L., Newman, R.M., Johnson, W.E.

(2013) PLoS Pathog 9: e1003352-e1003352

• PubMed: 23675300 
• DOI: 10.1371/journal.ppat.1003352
• Primary Citation of Related Structures:  
  4HTW


• PubMed Abstract: 
  

Retroviral capsid recognition by Trim5 blocks productive infection. Rhesus macaques harbor three functionally distinct Trim5 alleles: Trim5α(Q) , Trim5α(TFP) and Trim5(CypA) . Despite the high degree of amino acid identity between Trim5α(Q) and Trim5α(TFP) alleles, the Q/TFP polymorphism results in the differential restriction of some primate lentiviruses, suggesting these alleles differ in how they engage these capsids. Simian immunodeficiency virus of rhesus macaques (SIVmac) evolved to resist all three alleles. Thus, SIVmac provides a unique opportunity to study a virus in the context of the Trim5 repertoire that drove its evolution in vivo. We exploited the evolved rhesus Trim5α resistance of this capsid to identify gain-of-sensitivity mutations that distinguish targets between the Trim5α(Q) and Trim5α(TFP) alleles. While both alleles recognize the capsid surface, Trim5α(Q) and Trim5α(TFP) alleles differed in their ability to restrict a panel of capsid chimeras and single amino acid substitutions. When mapped onto the structure of the SIVmac239 capsid N-terminal domain, single amino acid substitutions affecting both alleles mapped to the β-hairpin. Given that none of the substitutions affected Trim5α(Q) alone, and the fact that the β-hairpin is conserved among retroviral capsids, we propose that the β-hairpin is a molecular pattern widely exploited by Trim5α proteins. Mutations specifically affecting rhesus Trim5α(TFP) (without affecting Trim5α(Q) ) surround a site of conservation unique to primate lentiviruses, overlapping the CPSF6 binding site. We believe targeting this site is an evolutionary innovation driven specifically by the emergence of primate lentiviruses in Africa during the last 12 million years. This modularity in targeting may be a general feature of Trim5 evolution, permitting different regions of the PRYSPRY domain to evolve independent interactions with capsid.

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Organizational Affiliation: 

Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag protein	A	143	Simian immunodeficiency virus	Mutation(s): 0  Gene Names: synthetic
Find proteins for Q8Q5M0 (Simian immunodeficiency virus) Explore Q8Q5M0  Go to UniProtKB:  Q8Q5M0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.293 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.614	α = 90
b = 56.663	β = 90
c = 102.566	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-02 
• Released Date: 2013-05-22 
Deposition Author(s): Schmidt, A.G.

Revision History 

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description