6BHT

HIV-1 CA hexamer in complex with IP6, orthorhombic crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.689 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A short, 14-amino-acid segment called SP1, located in the Gag structural protein <sup>1 </sup>, 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. rad82@cornell.edu.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.,Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.,Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA. opornillos@virginia.edu.,Department of Chemistry and Biochemistry, University of Delaware, Newport, DE, USA.,Institute of Science and Technology Austria, Klosterneuburg, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein p24
A, B, C, D, E, F, G, H, I, J, K, L
231Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 4 
Gene Names: gag
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12493
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.689 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 135.317α = 90.00
b = 137.173β = 90.00
c = 209.354γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01-AI129678
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU54-GM103297

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-08-15
    Type: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2018-09-05
    Type: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection