6BHR

HIV-1 immature CTD-SP1 hexamer in complex with IP6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Inositol phosphates are assembly co-factors for HIV-1.

Dick, R.A.Zadrozny, K.K.Xu, C.Schur, F.K.M.Lyddon, T.D.Ricana, C.L.Wagner, J.M.Perilla, J.R.Ganser-Pornillos, B.K.Johnson, M.C.Pornillos, O.Vogt, V.M.

(2018) Nature 560: 509-512

  • DOI: 10.1038/s41586-018-0396-4
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A short, 14-amino-acid segment called SP1, located in the Gag structural protein 1 , has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six- ...

    A short, 14-amino-acid segment called SP1, located in the Gag structural protein 1 , has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane 2,3 . Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors 4,5 . Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP 6 ) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP 6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP 6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP 6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein p24,Spacer peptide 1G95Human immunodeficiency virus type 1 BH10Mutation(s): 0 
Gene Names: gag
Find proteins for P03347 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03347 
Go to UniProtKB:  P03347
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.939α = 90
b = 70.939β = 90
c = 42.041γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI129678
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54-GM103297

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence