4J4J

Crystal structure of the APOBEC3F Vif binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1038/ncomms3593

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA dC->dU-editing enzyme APOBEC-3F
A, B
209Homo sapiensMutation(s): 0 
Gene Names: APOBEC3F
EC: 3.5.4.-
Find proteins for Q8IUX4 (Homo sapiens)
Go to Gene View: APOBEC3F
Go to UniProtKB:  Q8IUX4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.236 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 164.046α = 90.00
b = 164.046β = 90.00
c = 135.315γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
d*TREKdata reduction
PHASERphasing
PHENIXrefinement
d*TREKdata scaling
Executordata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references