› 5tkm

X-ray diffraction
1.9Å resolution

Crystal structure of human APOBEC3B N-terminal Domain

Released:
DOI: 10.2210/pdb5tkm/pdb
PDB entry 5tkm coloured by chain, front view.
PDB entry 5tkm coloured by chain, side view.
PDB entry 5tkm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation.
Xiao X, Yang H, Arutiunian V, Fang Y, Besse G, Morimoto C, Zirkle B, Chen XS
Nucleic Acids Res 45 7494-7506 (2017)
PMID: 28575276

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: 198 amino acids
Theoretical weight: 23.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q9UH17 (Residues: 1-191; Coverage: 50%)
Gene name: APOBEC3B
Sequence domains: Novel AID APOBEC clade 2

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 60.739Å b: 60.802Å c: 111.515Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.188 0.203
Expression system: Escherichia coli K-12

Quick links

Citations

18 citation in other articles

Enzyme cycling contributes to efficient induction of genome mutagenesis by the cytidine deaminase APOBEC3B.
Adolph et al. (2017)
17 more

8 mentions without citation

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