Crystal structure of the APOBEC3F Vif binding domain

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.241 

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Structural determinants of HIV-1 Vif susceptibility and DNA binding in APOBEC3F.

Siu, K.K.Sultana, A.Azimi, F.C.Lee, J.E.

(2013) Nat Commun 4: 2593-2593

  • DOI: https://doi.org/10.1038/ncomms3593
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The human APOBEC3 family of DNA cytosine deaminases serves as a front-line intrinsic immune response to inhibit the replication of diverse retroviruses. APOBEC3F and APOBEC3G are the most potent factors against HIV-1. As a countermeasure, HIV-1 viral infectivity factor (Vif) targets APOBEC3s for proteasomal degradation. Here we report the crystal structure of the Vif-binding domain in APOBEC3F and a novel assay to assess Vif-APOBEC3 binding. Our results point to an amphipathic surface that is conserved in APOBEC3s as critical for Vif susceptibility in APOBEC3F. Electrostatic interactions likely mediate Vif binding. Moreover, structure-guided mutagenesis reveals a straight ssDNA-binding groove distinct from the Vif-binding site, and an 'aromatic switch' is proposed to explain DNA substrate specificities across the APOBEC3 family. This study opens new lines of inquiry that will further our understanding of APOBEC3-mediated retroviral restriction and provides an accurate template for structure-guided development of inhibitors targeting the APOBEC3-Vif axis.

  • Organizational Affiliation

    Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Room 6316 Toronto, Ontario, Canada M5S 1A8.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA dC->dU-editing enzyme APOBEC-3F
A, B
209Homo sapiensMutation(s): 0 
Gene Names: APOBEC3F
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUX4 (Homo sapiens)
Explore Q8IUX4 
Go to UniProtKB:  Q8IUX4
GTEx:  ENSG00000128394 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IUX4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.241 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.046α = 90
b = 164.046β = 90
c = 135.315γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PDB_EXTRACTdata extraction
Executordata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations