6H09

HIV capsid hexamer with IP6 ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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


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:  
    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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gag polyproteinA219Human 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
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