5W4P

Structure of the E28A mutant of the HIV-1 capsid protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket.

Craveur, P.Gres, A.T.Kirby, K.A.Liu, D.Hammond, J.A.Deng, Y.Forli, S.Goodsell, D.S.Williamson, J.R.Sarafianos, S.G.Olson, A.J.

(2019) MBio 10: --

  • DOI: 10.1128/mBio.02858-18
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HIV-1 capsid protein (CA) plays critical roles in both early and late stages of the viral replication cycle. Mutagenesis and structural experiments have revealed that capsid core stability significantly affects uncoating and initiation of reverse tra ...

    HIV-1 capsid protein (CA) plays critical roles in both early and late stages of the viral replication cycle. Mutagenesis and structural experiments have revealed that capsid core stability significantly affects uncoating and initiation of reverse transcription in host cells. This has led to efforts in developing antivirals targeting CA and its assembly, although none of the currently identified compounds are used in the clinic for treatment of HIV infection. A specific interaction that is primarily present in pentameric interfaces in the HIV-1 capsid core was identified and is reported to be important for CA assembly. This is shown by multidisciplinary characterization of CA site-directed mutants using biochemical analysis of virus-like particle formation, transmission electron microscopy of in vitro assembly, crystallographic studies, and molecular dynamic simulations. The data are consistent with a model where a hydrogen bond between CA residues E28 and K30' from neighboring N-terminal domains (CA NTD s) is important for CA pentamer interactions during core assembly. This pentamer-preferred interaction forms part of an N -terminal d omain i nterface (NDI) pocket that is amenable to antiviral targeting. IMPORTANCE Precise assembly and disassembly of the HIV-1 capsid core are key to the success of viral replication. The forces that govern capsid core formation and dissociation involve intricate interactions between pentamers and hexamers formed by HIV-1 CA. We identified one particular interaction between E28 of one CA and K30' of the adjacent CA that appears more frequently in pentamers than in hexamers and that is important for capsid assembly. Targeting the corresponding site could lead to the development of antivirals which disrupt this interaction and affect capsid assembly.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.,Center for Integrative Proteomics Research, Rutgers State University, Piscataway, New Jersey, USA.,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA stefanos.sarafianos@emory.edu olson@scripps.edu.,Synsight, √Čvry, France.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.,Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, Missouri, USA.,Department of Biochemistry, University of Missouri, Columbia, Missouri, USA.,Department of Chemistry, University of Missouri, Columbia, Missouri, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA stefanos.sarafianos@emory.edu olson@scripps.edu.,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA.,Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein p24
A
231Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 1 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

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

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 92.672α = 90.00
b = 92.672β = 90.00
c = 57.969γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

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 General Medical Sciences (NIH/NIGMS)United StatesGM103368
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI120860

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-03-27
    Type: Data collection, Database references
  • Version 1.2: 2019-12-11
    Type: Author supporting evidence