4XXO

Crystal Structure of Human APOBEC3A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.843 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization.

Bohn, M.F.Shandilya, S.M.Silvas, T.V.Nalivaika, E.A.Kouno, T.Kelch, B.A.Ryder, S.P.Kurt-Yilmaz, N.Somasundaran, M.Schiffer, C.A.

(2015) Structure 23: 903-911

  • DOI: 10.1016/j.str.2015.03.016

  • PubMed Abstract: 
  • Deaminase activity mediated by the human APOBEC3 family of proteins contributes to genomic instability and cancer. APOBEC3A is by far the most active in this family and can cause rapid cell death when overexpressed, but in general how the activity of ...

    Deaminase activity mediated by the human APOBEC3 family of proteins contributes to genomic instability and cancer. APOBEC3A is by far the most active in this family and can cause rapid cell death when overexpressed, but in general how the activity of APOBEC3s is regulated on a molecular level is unclear. In this study, the biochemical and structural basis of APOBEC3A substrate binding and specificity is elucidated. We find that specific binding of single-stranded DNA is regulated by the cooperative dimerization of APOBEC3A. The crystal structure elucidates this homodimer as a symmetric domain swap of the N-terminal residues. This dimer interface provides insights into how cooperative protein-protein interactions may affect function in the APOBEC3 enzymes and provides a potential scaffold for strategies aimed at reducing their mutation load.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA; Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA.,Department of Pediatrics and Program in Molecular Medicine, University of Massachusetts Medical School Worcester, MA 01605, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA. Electronic address: celia.schiffer@umassmed.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA dC->dU-editing enzyme APOBEC-3A
A, B
203Homo sapiensMutation(s): 2 
Gene Names: APOBEC3A
EC: 3.5.4.38
Find proteins for P31941 (Homo sapiens)
Go to Gene View: APOBEC3A
Go to UniProtKB:  P31941
Small Molecules
Ligands 2 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
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.843 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.214 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.752α = 90.00
b = 94.752β = 90.00
c = 213.962γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXphasing
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM091743

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-13
    Type: Database references
  • Version 1.2: 2015-05-20
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Source and taxonomy