› 5w0u

X-ray diffraction
2.9Å resolution

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

Released:
DOI: 10.2210/pdb5w0u/pdb
PDB entry 5w0u coloured by chain, front view.
PDB entry 5w0u coloured by chain, side view.
PDB entry 5w0u 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

Assemblies composition:
hetero trimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-199485 (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: 61.66 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P0AEX9 (Residues: 27-392; Coverage: 99%)
  • Canonical: Q9GZX7 (Residues: 13-181; Coverage: 85%)
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

4 bound ligands:
Ligand ZN 2 x ZN
Ligand DCM 2 x DCM
Ligand CA 2 x CA
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P2
Unit cell:
a: 125.005Å b: 39.777Å c: 153.935Å
α: 90° β: 90.14° γ: 90°
R-values:
R R work R free
0.252 0.251 0.281
Expression system: Spodoptera frugiperda

Quick links

Citations

28 review citations

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

6 mentions without citation

Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination.
Pecori et al. (2022)
5 more