› 5cqd

X-ray diffraction
2.08Å resolution

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B

Released:
DOI: 10.2210/pdb5cqd/pdb
PDB entry 5cqd coloured by chain, front view.
PDB entry 5cqd coloured by chain, side view.
PDB entry 5cqd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain.
Shi K, Carpenter MA, Kurahashi K, Harris RS, Aihara H
J Biol Chem 290 28120-28130 (2015)
PMID: 26416889

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:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193726 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA dC->dU-editing enzyme APOBEC-3B Chains: A, C
Molecule details ›
Chains: A, C
Length: 186 amino acids
Theoretical weight: 21.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UH17 (Residues: 187-378; Coverage: 48%)
Gene name: APOBEC3B
Sequence domains: APOBEC-like C-terminal domain

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 53.44Å b: 50.84Å c: 70.15Å
α: 90° β: 100.83° γ: 90°
R-values:
R R work R free
0.19 0.188 0.227
Expression system: Escherichia coli

Quick links

Citations

10 review citations

The APOBEC Protein Family: United by Structure, Divergent in Function.
Salter et al. (2016)
9 more

5 mentions without citation

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