6BHT | pdb_00006bht

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.255 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.7 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: https://doi.org/10.1038/s41586-018-0396-4
  • Primary Citation Related Structures: 
    6BHR, 6BHS, 6BHT

  • 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-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.

Macromolecule Content 

  • Total Structure Weight: 308.18 kDa 
  • Atom Count: 19,794 
  • Modeled Residue Count: 2,551 
  • Deposited Residue Count: 2,772 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein p24
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
231Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 4 
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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.255 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.317α = 90
b = 137.173β = 90
c = 209.354γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2018-09-05
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2020-10-14
    Changes: Structure summary
  • Version 1.6: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.7: 2024-11-06
    Changes: Structure summary