4XFZ

Structure of the native full-length HIV-1 capsid protein in complex with PF-3450074 (PF74)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

STRUCTURAL VIROLOGY. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability.

Gres, A.T.Kirby, K.A.KewalRamani, V.N.Tanner, J.J.Pornillos, O.Sarafianos, S.G.

(2015) Science 349: 99-103

  • DOI: 10.1126/science.aaa5936
  • Primary Citation of Related Structures:  4XFX, 4XFY

  • PubMed Abstract: 
  • The detailed molecular interactions between native HIV-1 capsid protein (CA) hexamers that shield the viral genome and proteins have been elusive. We report crystal structures describing interactions between CA monomers related by sixfold symmetry wi ...

    The detailed molecular interactions between native HIV-1 capsid protein (CA) hexamers that shield the viral genome and proteins have been elusive. We report crystal structures describing interactions between CA monomers related by sixfold symmetry within hexamers (intrahexamer) and threefold and twofold symmetry between neighboring hexamers (interhexamer). The structures describe how CA builds hexagonal lattices, the foundation of mature capsids. Lattice structure depends on an adaptable hydration layer modulating interactions among CA molecules. Disruption of this layer alters interhexamer interfaces, highlighting an inherent structural variability. A CA-targeting antiviral affects capsid stability by binding across CA molecules and subtly altering interhexamer interfaces remote to the ligand-binding site. Inherent structural plasticity, hydration layer rearrangement, and effector binding affect capsid stability and have functional implications for the retroviral life cycle.


    Organizational Affiliation

    Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA. Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 capsid protein
A
231Human immunodeficiency virus type 1 group M subtype BGene Names: gag
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12493
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

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Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
1B0
Query on 1B0

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Download 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.210 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 92.181α = 90.00
b = 92.181β = 90.00
c = 56.976γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI076119
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI099284
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI100890
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI112417
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103368

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-17
    Type: Database references, Refinement description, Structure summary
  • Version 1.2: 2015-07-15
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Source and taxonomy