› 5sxg

X-ray diffraction
1.93Å resolution

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B

Released:
DOI: 10.2210/pdb5sxg/pdb
PDB entry 5sxg coloured by chain, front view.
PDB entry 5sxg coloured by chain, side view.
PDB entry 5sxg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.
Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H
Sci Rep 7 17415 (2017)
PMID: 29234087

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, B
Molecule details ›
Chains: A, B
Length: 185 amino acids
Theoretical weight: 21.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UH17 (Residues: 191-378; Coverage: 47%)
Gene name: APOBEC3B
Sequence domains: APOBEC-like C-terminal domain

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand PDO 6 x PDO
Ligand IMD 1 x IMD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 44.39Å b: 50.8Å c: 76.89Å
α: 90° β: 102.86° γ: 90°
R-values:
R R work R free
0.178 0.177 0.21
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands.
Salter et al. (2018)
3 more

1 mention without citation

Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.
Shi et al. (2017)