› 5td5

X-ray diffraction
1.72Å resolution

Crystal Structure of Human APOBEC3B variant complexed with ssDNA

Released:
DOI: 10.2210/pdb5td5/pdb
PDB entry 5td5 coloured by chain, front view.
PDB entry 5td5 coloured by chain, side view.
PDB entry 5td5 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:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119151 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA dC->dU-editing enzyme APOBEC-3B Chain: A
Molecule details ›
Chain: A
Length: 190 amino acids
Theoretical weight: 22.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UH17 (Residues: 187-378; Coverage: 47%)
Gene name: APOBEC3B
Sequence domains: APOBEC-like C-terminal domain
DNA (5'-D(P*TP*TP*CP*AP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 7 nucleotides
Theoretical weight: 2.08 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand IOD 9 x IOD
Ligand EDO 6 x EDO
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P6422
Unit cell:
a: 96.411Å b: 96.411Å c: 84.875Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.18 0.209
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

22 review citations

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

20 mentions without citation

APOBEC3s: DNA-editing human cytidine deaminases.
Silvas et al. (2019)
19 more