4U0E

Hexameric HIV-1 CA in complex with PF3450074

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    4U0A, 4U0B, 4U0C, 4U0D, 4U0E, 4U0F

  • 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), and t ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein p24 A231Human 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
1B0
Query on 1B0
Download Ideal Coordinates CCD File 
A
N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE
C27 H27 N3 O2
ACDFWSNAQWFRRF-VWLOTQADSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1B0Kd:  120   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.21α = 90
b = 91.21β = 90
c = 56.34γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
iMOSFLMdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release