6ECO

Hexamer-2-Foldon HIV-1 capsid platform


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.288 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Modular HIV-1 Capsid Assemblies Reveal Diverse Host-Capsid Recognition Mechanisms.

Summers, B.J.Digianantonio, K.M.Smaga, S.S.Huang, P.T.Zhou, K.Gerber, E.E.Wang, W.Xiong, Y.

(2019) Cell Host Microbe 26: 203-216.e6

  • DOI: 10.1016/j.chom.2019.07.007
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The HIV-1 capsid is an ordered protein shell that houses the viral genome during early infection. Its expansive surface consists of an ordered and interfacing array of capsid protein hexamers and pentamers that are recognized by numerous cellular pro ...

    The HIV-1 capsid is an ordered protein shell that houses the viral genome during early infection. Its expansive surface consists of an ordered and interfacing array of capsid protein hexamers and pentamers that are recognized by numerous cellular proteins. Many of these proteins recognize specific, assembled capsid interfaces not present in unassembled capsid subunits. We used protein-engineering tools to capture diverse capsid assembly intermediates. We built a repertoire of capsid assemblies (ranging from two to 42 capsid protein molecules) that recreate the various surfaces in infectious capsids. These assemblies reveal unique capsid-targeting mechanisms for each of the anti-HIV factors, TRIMCyp, MxB, and TRIM5α, linked to inhibition of virus uncoating and nuclear entry, as well as the HIV-1 cofactor FEZ1 that facilitates virus intracellular trafficking. This capsid assembly repertoire enables elucidation of capsid recognition modes by known capsid-interacting factors, identification of new capsid-interacting factors, and potentially, development of capsid-targeting therapeutics.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA. Electronic address: yong.xiong@yale.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 capsid platform protein
A
253Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: gag
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12493

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 capsid platform protein
D
221Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: gag
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12493
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.288 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.25α = 90
b = 95.25β = 90
c = 122.57γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5P50GM082251-12

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence