Crystal structure of APOBEC3H

Experimental Data Snapshot

  • Resolution: 2.49 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

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Understanding the Structure, Multimerization, Subcellular Localization and mC Selectivity of a Genomic Mutator and Anti-HIV Factor APOBEC3H.

Ito, F.Yang, H.Xiao, X.Li, S.X.Wolfe, A.Zirkle, B.Arutiunian, V.Chen, X.S.

(2018) Sci Rep 8: 3763-3763

  • DOI: https://doi.org/10.1038/s41598-018-21955-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    APOBEC3H (A3H) is a member of the APOBEC3 subfamily of DNA cytosine deaminases that are important for innate immune defense and have been implicated in cancer biogenesis. To understand the structural basis for A3H biochemical function, we determined a high-resolution structure of human A3H and performed extensive biochemical analysis. The 2.49 Å crystal structure reveals a uniquely long C-terminal helix 6 (h6), a disrupted β5 strand of the canonical five-stranded β-sheet core, and a long loop 1 around the Zn-active center. Mutation of a loop 7 residue, W115, disrupted the RNA-mediated dimerization of A3H yielding an RNA-free monomeric form that still possessed nucleic acid binding and deaminase activity. A3H expressed in HEK293T cells showed RNA dependent HMW complex formation and RNase A-dependent deaminase activity. A3H has a highly positively charged surface surrounding the Zn-active center, and multiple positively charged residues within this charged surface play an important role in the RNA-mediated HMW formation and deaminase inhibition. Furthermore, these positively charged residues affect subcellular localization of A3H between the nucleus and cytosol. Finally, we have identified multiple residues of loop 1 and 7 that contribute to the overall deaminase activity and the methylcytosine selectivity.

  • Organizational Affiliation

    Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
181Homo sapiensMutation(s): 0 
Gene Names: APOBEC3H
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NTF7 (Homo sapiens)
Explore Q6NTF7 
Go to UniProtKB:  Q6NTF7
GTEx:  ENSG00000100298 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NTF7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.49 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.749α = 90
b = 65.006β = 90.08
c = 65.54γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary