5HGL

Hexameric HIV-1 CA, open conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis.

Jacques, D.A.McEwan, W.A.Hilditch, L.Price, A.J.Towers, G.J.James, L.C.

(2016) Nature 536: 349-353

  • DOI: 10.1038/nature19098
  • Primary Citation of Related Structures:  5JPA, 5HGK, 5HGM, 5HGN, 5HGO, 5HGP

  • PubMed Abstract: 
  • During the early stages of infection, the HIV-1 capsid protects viral components from cytosolic sensors and nucleases such as cGAS and TREX, respectively, while allowing access to nucleotides for efficient reverse transcription. Here we show that eac ...

    During the early stages of infection, the HIV-1 capsid protects viral components from cytosolic sensors and nucleases such as cGAS and TREX, respectively, while allowing access to nucleotides for efficient reverse transcription. Here we show that each capsid hexamer has a size-selective pore bound by a ring of six arginine residues and a 'molecular iris' formed by the amino-terminal β-hairpin. The arginine ring creates a strongly positively charged channel that recruits the four nucleotides with on-rates that approach diffusion limits. Progressive removal of pore arginines results in a dose-dependent and concomitant decrease in nucleotide affinity, reverse transcription and infectivity. This positively charged channel is universally conserved in lentiviral capsids despite the fact that it is strongly destabilizing without nucleotides to counteract charge repulsion. We also describe a channel inhibitor, hexacarboxybenzene, which competes for nucleotide binding and efficiently blocks encapsidated reverse transcription, demonstrating the tractability of the pore as a novel drug target.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein P24
A, B, C, D, E, F
231Human immunodeficiency virus type 1 group M subtype BGene Names: gag
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12493
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
1B0
Query on 1B0

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE
C27 H27 N3 O2
ACDFWSNAQWFRRF-VWLOTQADSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.250 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 89.690α = 90.00
b = 159.270β = 90.00
c = 249.399γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MAR345dtbdata collection
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Medical Research Council (United Kingdom)United KingdomUK; U105181010
European Research CouncilUnited Kingdom281627 -IAI
National Health and Medical Research CouncilAustraliaGNT1036521

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-24
    Type: Database references
  • Version 1.2: 2016-08-31
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence
  • Version 1.4: 2018-01-24
    Type: Source and taxonomy