› 5keg

X-ray diffraction
2.2Å resolution

Crystal structure of APOBEC3A in complex with a single-stranded DNA

Released:
DOI: 10.2210/pdb5keg/pdb
PDB entry 5keg coloured by chain, front view.
PDB entry 5keg coloured by chain, side view.
PDB entry 5keg coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.
Kouno T, Silvas TV, Hilbert BJ, Shandilya SMD, Bohn MF, Kelch BA, Royer WE, Somasundaran M, Kurt Yilmaz N, Matsuo H, Schiffer CA
Nat Commun 8 15024 (2017)
PMID: 28452355

Function and Biology Details

Reaction catalysed: 
Cytosine in single-stranded DNA + H(2)O = uracil in single-stranded DNA + NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118909 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA dC->dU-editing enzyme APOBEC-3A Chain: A
Molecule details ›
Chain: A
Length: 203 amino acids
Theoretical weight: 23.3 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P31941 (Residues: 1-199; Coverage: 100%)
Gene name: APOBEC3A
Sequence domains: APOBEC-like C-terminal domain
DNA (5'-D(*TP*TP*CP*TP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 15 nucleotides
Theoretical weight: 4.5 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand CA 1 x CA
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: I222
Unit cell:
a: 56.583Å b: 72.666Å c: 114.971Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.177 0.225
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

14 review citations

APOBEC Enzymes as Targets for Virus and Cancer Therapy.
Olson et al. (2018)
13 more

28 mentions without citation

Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination.
Pecori et al. (2022)
27 more