7QDF

Hexameric HIV-1 (M-group) CA R120 mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evasion of cGAS and TRIM5 defines pandemic HIV.

Zuliani-Alvarez, L.Govasli, M.L.Rasaiyaah, J.Monit, C.Perry, S.O.Sumner, R.P.McAlpine-Scott, S.Dickson, C.Rifat Faysal, K.M.Hilditch, L.Miles, R.J.Bibollet-Ruche, F.Hahn, B.H.Boecking, T.Pinotsis, N.James, L.C.Jacques, D.A.Towers, G.J.

(2022) Nat Microbiol 7: 1762-1776

  • DOI: https://doi.org/10.1038/s41564-022-01247-0
  • Primary Citation of Related Structures:  
    7QDF, 7T12, 7T13, 7T14, 7T15, 8D3B

  • PubMed Abstract: 

    Of the 13 known independent zoonoses of simian immunodeficiency viruses to humans, only one, leading to human immunodeficiency virus (HIV) type 1(M) has become pandemic, causing over 80 million human infections. To understand the specific features associated with pandemic human-to-human HIV spread, we compared replication of HIV-1(M) with non-pandemic HIV-(O) and HIV-2 strains in myeloid cell models. We found that non-pandemic HIV lineages replicate less well than HIV-1(M) owing to activation of cGAS and TRIM5-mediated antiviral responses. We applied phylogenetic and X-ray crystallography structural analyses to identify differences between pandemic and non-pandemic HIV capsids. We found that genetic reversal of two specific amino acid adaptations in HIV-1(M) enables activation of TRIM5, cGAS and innate immune responses. We propose a model in which the parental lineage of pandemic HIV-1(M) evolved a capsid that prevents cGAS and TRIM5 triggering, thereby allowing silent replication in myeloid cells. We hypothesize that this capsid adaptation promotes human-to-human spread through avoidance of innate immune response activation.


  • Organizational Affiliation

    Division of Infection and Immunity, UCL, London, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag polyproteinA [auth AAA]232Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 0 
Gene Names: gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12493 
Go to UniProtKB:  P12493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12493
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
B [auth AAA],
C [auth AAA]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
BME
Query on BME

Download Ideal Coordinates CCD File 
I [auth AAA]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.242 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.36α = 90
b = 92.36β = 90
c = 57.44γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP180101384
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1158338
Wellcome TrustUnited Kingdom214344/Z/18/Z
Wellcome TrustUnited Kingdom108183
Wellcome TrustUnited Kingdom220863
European Research Council (ERC)European Union339223

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description