› 5sww

X-ray diffraction
3.15Å resolution

Crystal Structure of Human APOBEC3A complexed with ssDNA

Released:
DOI: 10.2210/pdb5sww/pdb
PDB entry 5sww coloured by chain, front view.
PDB entry 5sww coloured by chain, side view.
PDB entry 5sww coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi K, Salamango DJ, McCann JL, Starrett GJ, Duffy JV, Demir Ö, Amaro RE, Harki DA, Harris RS, Aihara H
Nat Struct Mol Biol 24 131-139 (2017)
PMID: 27991903

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-119123 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA dC->dU-editing enzyme APOBEC-3A Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 204 amino acids
Theoretical weight: 23.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P31941 (Residues: 1-196; Coverage: 99%)
Gene name: APOBEC3A
Sequence domains: APOBEC-like C-terminal domain
DNA 15-Mer Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 15 nucleotides
Theoretical weight: 4.67 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P2221
Unit cell:
a: 90.148Å b: 90.199Å c: 167.257Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.21 0.263
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

21 review citations

Base editing: advances and therapeutic opportunities.
Porto et al. (2020)
20 more

32 mentions without citation

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