Zinc-Free APOBEC3F Catalytic Domain Crystal Structure

Experimental Data Snapshot

  • Resolution: 1.92 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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This is version 1.2 of the entry. See complete history


1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure.

Shaban, N.M.Shi, K.Li, M.Aihara, H.Harris, R.S.

(2016) J Mol Biol 428: 2307-2316

  • DOI: https://doi.org/10.1016/j.jmb.2016.04.026
  • Primary Citation of Related Structures:  
    5HX4, 5HX5

  • PubMed Abstract: 

    The APOBEC3 family of DNA cytosine deaminases is capable of restricting the replication of HIV-1 and other pathogens. Here, we report a 1.92 Å resolution crystal structure of the Vif-binding and catalytic domain of APOBEC3F (A3F). This structure is distinct from the previously published APOBEC and phylogenetically related deaminase structures, as it is the first without zinc in the active site. We determined an additional structure containing zinc in the same crystal form that allows direct comparison with the zinc-free structure. In the absence of zinc, the conserved active site residues that normally participate in zinc coordination show unique conformations, including a 90 degree rotation of His249 and disulfide bond formation between Cys280 and Cys283. We found that zinc coordination is influenced by pH, and treating the protein at low pH in crystallization buffer is sufficient to remove zinc. Zinc coordination and catalytic activity are reconstituted with the addition of zinc only in a reduced environment likely due to the two active site cysteines readily forming a disulfide bond when not coordinating zinc. We show that the enzyme is active in the presence of zinc and cobalt but not with other divalent metals. These results unexpectedly demonstrate that zinc is not required for the structural integrity of A3F and suggest that metal coordination may be a strategy for regulating the activity of A3F and related deaminases.

  • Organizational Affiliation

    Department of Biochemistry, Molecular Biology, and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: nmshaban@umn.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA dC->dU-editing enzyme APOBEC-3F
A, B
199Homo sapiensMutation(s): 9 
Gene Names: APOBEC3F
EC: 3.5.4
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: 1.92 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.1α = 90
b = 51.27β = 90.85
c = 99.77γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description