4IOU

Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.751 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the DNA Cytosine Deaminase APOBEC3F: The Catalytically Active and HIV-1 Vif-Binding Domain.

Bohn, M.F.Shandilya, S.M.Albin, J.S.Kouno, T.Anderson, B.D.McDougle, R.M.Carpenter, M.A.Rathore, A.Evans, L.Davis, A.N.Zhang, J.Lu, Y.Somasundaran, M.Matsuo, H.Harris, R.S.Schiffer, C.A.

(2013) Structure 21: 1042-1050

  • DOI: 10.1016/j.str.2013.04.010

  • PubMed Abstract: 
  • Human APOBEC3F is an antiretroviral single-strand DNA cytosine deaminase, susceptible to degradation by the HIV-1 protein Vif. In this study the crystal structure of the HIV Vif binding, catalytically active, C-terminal domain of APOBEC3F (A3F-CTD) w ...

    Human APOBEC3F is an antiretroviral single-strand DNA cytosine deaminase, susceptible to degradation by the HIV-1 protein Vif. In this study the crystal structure of the HIV Vif binding, catalytically active, C-terminal domain of APOBEC3F (A3F-CTD) was determined. The A3F-CTD shares structural motifs with portions of APOBEC3G-CTD, APOBEC3C, and APOBEC2. Residues identified to be critical for Vif-dependent degradation of APOBEC3F all fit within a predominantly negatively charged contiguous region on the surface of A3F-CTD. Specific sequence motifs, previously shown to play a role in Vif susceptibility and virion encapsidation, are conserved across APOBEC3s and between APOBEC3s and HIV-1 Vif. In this structure these motifs pack against each other at intermolecular interfaces, providing potential insights both into APOBEC3 oligomerization and Vif interactions.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA dC->dU-editing enzyme APOBEC-3F
A, B, C, D
199Homo sapiensMutation(s): 11 
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, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.751 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.790α = 110.75
b = 66.910β = 94.41
c = 75.640γ = 108.83
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
REFMACrefinement
Locallydata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references, Other, Refinement description
  • Version 1.2: 2013-07-03
    Type: Database references