6NIL

cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of antagonism of human APOBEC3F by HIV-1 Vif.

Hu, Y.Desimmie, B.A.Nguyen, H.C.Ziegler, S.J.Cheng, T.C.Chen, J.Wang, J.Wang, H.Zhang, K.Pathak, V.K.Xiong, Y.

(2019) Nat Struct Mol Biol 26: 1176-1183

  • DOI: https://doi.org/10.1038/s41594-019-0343-6
  • Primary Citation of Related Structures:  
    6NIL

  • PubMed Abstract: 

    HIV-1 virion infectivity factor (Vif) promotes degradation of the antiviral APOBEC3 (A3) proteins through the host ubiquitin-proteasome pathway to enable viral immune evasion. Disrupting Vif-A3 interactions to reinstate the A3-catalyzed suppression of human immunodeficiency virus type 1 (HIV-1) replication is a potential approach for antiviral therapeutics. However, the molecular mechanisms by which Vif recognizes A3 proteins remain elusive. Here we report a cryo-EM structure of the Vif-targeted C-terminal domain of human A3F in complex with HIV-1 Vif and the cellular cofactor core-binding factor beta (CBFβ) at 3.9-Å resolution. The structure shows that Vif and CBFβ form a platform to recruit A3F, revealing a direct A3F-recruiting role of CBFβ beyond Vif stabilization, and captures multiple independent A3F-Vif interfaces. Together with our biochemical and cellular studies, our structural findings establish the molecular determinants that are critical for Vif-mediated neutralization of A3F and provide a comprehensive framework of how HIV-1 Vif hijacks the host protein degradation machinery to counteract viral restriction by A3F.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA dC->dU-editing enzyme APOBEC-3F
A, D, G, J
207Homo sapiensMutation(s): 10 
Gene Names: APOBEC3F
EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUX4 (Homo sapiens)
Explore Q8IUX4 
Go to UniProtKB:  Q8IUX4
PHAROS:  Q8IUX4
GTEx:  ENSG00000128394 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IUX4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Core-binding factor subunit beta
B, E, H, K
151Homo sapiensMutation(s): 0 
Gene Names: CBFB
UniProt & NIH Common Fund Data Resources
Find proteins for Q13951 (Homo sapiens)
Explore Q13951 
Go to UniProtKB:  Q13951
PHAROS:  Q13951
GTEx:  ENSG00000067955 
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UniProt GroupQ13951
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Virion infectivity factor
C, F, I, L
138Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: vif
UniProt
Find proteins for P12504 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12504 
Go to UniProtKB:  P12504
Entity Groups  
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UniProt GroupP12504
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesAI116313

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references