› 5cqh

X-ray diffraction
1.73Å resolution

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B

Released:
DOI: 10.2210/pdb5cqh/pdb
PDB entry 5cqh coloured by chain, front view.
PDB entry 5cqh coloured by chain, side view.
PDB entry 5cqh 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 Chain: A
Molecule details ›
Chain: A
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

4 bound ligands:
Ligand ZN 1 x ZN
Ligand DC 1 x DC
Ligand CL 1 x CL
Ligand EDO 4 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 50.843Å b: 52.448Å c: 68.035Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.152 0.186
Expression system: Escherichia coli

Quick links

Citations

12 review citations

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

7 mentions without citation

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
Shi et al. (2017)
6 more