4U0F

Hexameric HIV-1 CA in Complex with BI-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly.

Price, A.J.Jacques, D.A.McEwan, W.A.Fletcher, A.J.Essig, S.Chin, J.W.Halambage, U.D.Aiken, C.James, L.C.

(2014) PLoS Pathog 10: e1004459-e1004459

  • DOI: 10.1371/journal.ppat.1004459
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The HIV-1 capsid is involved in all infectious steps from reverse transcription to integration site selection, and is the target of multiple host cell and pharmacologic ligands. However, structural studies have been limited to capsid monomers (CA), a ...

    The HIV-1 capsid is involved in all infectious steps from reverse transcription to integration site selection, and is the target of multiple host cell and pharmacologic ligands. However, structural studies have been limited to capsid monomers (CA), and the mechanistic basis for how these ligands influence infection is not well understood. Here we show that a multi-subunit interface formed exclusively within CA hexamers mediates binding to linear epitopes within cellular cofactors NUP153 and CPSF6, and is competed for by the antiretroviral compounds PF74 and BI-2. Each ligand is anchored via a shared phenylalanine-glycine (FG) motif to a pocket within the N-terminal domain of one monomer, and all but BI-2 also make essential interactions across the N-terminal domain: C-terminal domain (NTD:CTD) interface to a second monomer. Dissociation of hexamer into CA monomers prevents high affinity interaction with CPSF6 and PF74, and abolishes binding to NUP153. The second interface is conformationally dynamic, but binding of NUP153 or CPSF6 peptides is accommodated by only one conformation. NUP153 and CPSF6 have overlapping binding sites, but each makes unique CA interactions that, when mutated selectively, perturb cofactor dependency. These results reveal that multiple ligands share an overlapping interface in HIV-1 capsid that is lost upon viral disassembly.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Cambridge, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein p24A231Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 4 
Gene Names: gag
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12493 
Go to UniProtKB:  P12493
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3A8
Query on 3A8

Download CCD File 
A
(4S)-4-(4-hydroxyphenyl)-3-phenyl-4,5-dihydropyrrolo[3,4-c]pyrazol-6(1H)-one
C17 H13 N3 O2
RPZICXOAOIBXJT-AWEZNQCLSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3A8Kd:  1200   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.88α = 90
b = 90.88β = 90
c = 56.58γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Experimental preparation