6H09 | pdb_00006h09

HIV capsid hexamer with IP6 ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.266 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6H09

This is version 1.4 of the entry. See complete history

Literature

IP6 is an HIV pocket factor that prevents capsid collapse and promotes DNA synthesis.

Mallery, D.L.Marquez, C.L.McEwan, W.A.Dickson, C.F.Jacques, D.A.Anandapadamanaban, M.Bichel, K.Towers, G.J.Saiardi, A.Bocking, T.James, L.C.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.35335
  • Primary Citation Related Structures: 
    6ES8, 6H09

  • PubMed Abstract: 

    The HIV capsid is semipermeable and covered in electropositive pores that are essential for viral DNA synthesis and infection. Here, we show that these pores bind the abundant cellular polyanion IP 6 , transforming viral stability from minutes to hours and allowing newly synthesised DNA to accumulate inside the capsid. An arginine ring within the pore coordinates IP 6 , which strengthens capsid hexamers by almost 10°C. Single molecule measurements demonstrate that this renders native HIV capsids highly stable and protected from spontaneous collapse. Moreover, encapsidated reverse transcription assays reveal that, once stabilised by IP 6 , the accumulation of new viral DNA inside the capsid increases >100 fold. Remarkably, isotopic labelling of inositol in virus-producing cells reveals that HIV selectively packages over 300 IP 6 molecules per infectious virion. We propose that HIV recruits IP 6 to regulate capsid stability and uncoating, analogous to picornavirus pocket factors. HIV-1/IP 6 /capsid/co-factor/reverse transcription.


  • Organizational Affiliation
    • Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 25.16 kDa 
  • Atom Count: 1,830 
  • Modeled Residue Count: 205 
  • Deposited Residue Count: 219 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gag polyprotein219Human 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP

Query on IHP



Download:Ideal Coordinates CCD File
B [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.266 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.099α = 90
b = 91.099β = 90
c = 57.111γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2018-08-15 
  • Deposition Author(s): James, L.C.

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2020-10-07
    Changes: Derived calculations, Structure summary
  • Version 1.3: 2025-04-09
    Changes: Advisory, Data collection, Database references, Structure summary
  • Version 1.4: 2025-10-01
    Changes: Derived calculations, Structure summary