HIV capsid hexamer with IP6 ligand

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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 of 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

    EMBL Australia Node, Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag polyprotein219Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 0 
Gene Names: gag
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IHP

Download Ideal Coordinates CCD File 
C6 H18 O24 P6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • 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
iMOSFLMdata reduction
pointlessdata scaling

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