6ES8

HIV capsid hexamer with IP6 ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.7554/eLife.35335
  • Primary Citation of Related Structures:  

  • 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 <sub>6 </sub>, transforming viral stability from min ...

    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.,Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom.,Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.,ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney, Australia.,Division of Infection and Immunity, University College London, London, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag protein
A
219Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12497
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download SDF File 
Download CCD File 
A
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 91.299α = 90.00
b = 91.299β = 90.00
c = 57.201γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-10-19 
  • Released Date: 2018-08-15 
  • Deposition Author(s): James, L.C.

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release