› 5w1c

X-ray diffraction
3.18Å resolution

Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with cytidine

Released:
DOI: 10.2210/pdb5w1c/pdb
PDB entry 5w1c coloured by chain, front view.
PDB entry 5w1c coloured by chain, side view.
PDB entry 5w1c coloured by chain, top view.
Source organisms:
Primary publication:
AID Recognizes Structured DNA for Class Switch Recombination.
Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H
Mol Cell 67 361-373.e4 (2017)
PMID: 28757211

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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-199486 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Maltose/maltodextrin-binding periplasmic protein; Single-stranded DNA cytosine deaminase Chains: A, B
Molecule details ›
Chains: A, B
Length: 549 amino acids
Theoretical weight: 62.08 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P0AEX9 (Residues: 27-392; Coverage: 99%)
  • Canonical: Q9GZX7 (Residues: 5-181; Coverage: 89%)
Gene names: AICDA, AID, JW3994, b4034, malE
Sequence domains:
DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3') Chain: G
Molecule details ›
Chain: G
Length: 12 nucleotides
Theoretical weight: 3.64 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand CTN 2 x CTN
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P2
Unit cell:
a: 125.456Å b: 39.824Å c: 155.304Å
α: 90° β: 90.27° γ: 90°
R-values:
R R work R free
0.234 0.232 0.27
Expression system: Spodoptera frugiperda

Quick links

Citations

29 review citations

V(D)J recombination, somatic hypermutation and class switch recombination of immunoglobulins: mechanism and regulation.
Chi et al. (2020)
28 more

5 mentions without citation

Insights into the Structures and Multimeric Status of APOBEC Proteins Involved in Viral Restriction and Other Cellular Functions.
Chen XS. (2021)
4 more