7QDF | pdb_00007qdf

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.278 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.243 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7QDF

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 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.

Macromolecule Content 

  • Total Structure Weight: 26.3 kDa 
  • Atom Count: 1,772 
  • Modeled Residue Count: 222 
  • Deposited Residue Count: 232 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.243 (DCC) 
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