2X83

Evolutionary basis of HIV restriction by the antiretroviral TRIMCyp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Conformational adaptation of Asian macaque TRIMCyp directs lineage specific antiviral activity.

Ylinen, L.M.Price, A.J.Rasaiyaah, J.Hue, S.Rose, N.J.Marzetta, F.James, L.C.Towers, G.J.

(2010) Plos Pathog. 6: e1001062-e1001062

  • DOI: 10.1371/journal.ppat.1001062
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • TRIMCyps are anti-retroviral proteins that have arisen independently in New World and Old World primates. All TRIMCyps comprise a CypA domain fused to the tripartite domains of TRIM5alpha but they have distinct lentiviral specificities, conferring HI ...

    TRIMCyps are anti-retroviral proteins that have arisen independently in New World and Old World primates. All TRIMCyps comprise a CypA domain fused to the tripartite domains of TRIM5alpha but they have distinct lentiviral specificities, conferring HIV-1 restriction in New World owl monkeys and HIV-2 restriction in Old World rhesus macaques. Here we provide evidence that Asian macaque TRIMCyps have acquired changes that switch restriction specificity between different lentiviral lineages, resulting in species-specific alleles that target different viruses. Structural, thermodynamic and viral restriction analysis suggests that a single mutation in the Cyp domain, R69H, occurred early in macaque TRIMCyp evolution, expanding restriction specificity to the lentiviral lineages found in African green monkeys, sooty mangabeys and chimpanzees. Subsequent mutations have enhanced restriction to particular viruses but at the cost of broad specificity. We reveal how specificity is altered by a scaffold mutation, E143K, that modifies surface electrostatics and propagates conformational changes into the active site. Our results suggest that lentiviruses may have been important pathogens in Asian macaques despite the fact that there are no reported lentiviral infections in current macaque populations.


    Organizational Affiliation

    University College London Medical Research Council Centre for Medical Molecular Virology, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 CAPSID
A, C
146Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag
Find proteins for E9MJX7 (Human immunodeficiency virus 1)
Go to UniProtKB:  E9MJX7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRIM5/CypA fusion protein
B, D
163Macaca fascicularisMutation(s): 0 
Find proteins for B0ZE32 (Macaca fascicularis)
Go to UniProtKB:  B0ZE32
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.520α = 90.00
b = 110.150β = 101.59
c = 67.760γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-04-24
    Type: Advisory, Data collection, Database references, Experimental preparation, Other, Source and taxonomy, Structure summary