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

Experimental Data Snapshot

  • Resolution: 3.61 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.276 

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AID Recognizes Structured DNA for Class Switch Recombination.

Qiao, Q.Wang, L.Meng, F.L.Hwang, J.K.Alt, F.W.Wu, H.

(2017) Mol Cell 67: 361-373.e4

  • DOI: https://doi.org/10.1016/j.molcel.2017.06.034
  • Primary Citation of Related Structures:  
    5W0R, 5W0U, 5W0Z, 5W1C

  • PubMed Abstract: 

    Activation-induced cytidine deaminase (AID) initiates both class switch recombination (CSR) and somatic hypermutation (SHM) in antibody diversification. Mechanisms of AID targeting and catalysis remain elusive despite its critical immunological roles and off-target effects in tumorigenesis. Here, we produced active human AID and revealed its preferred recognition and deamination of structured substrates. G-quadruplex (G4)-containing substrates mimicking the mammalian immunoglobulin switch regions are particularly good AID substrates in vitro. By solving crystal structures of maltose binding protein (MBP)-fused AID alone and in complex with deoxycytidine monophosphate, we surprisingly identify a bifurcated substrate-binding surface that explains structured substrate recognition by capturing two adjacent single-stranded overhangs simultaneously. Moreover, G4 substrates induce cooperative AID oligomerization. Structure-based mutations that disrupt bifurcated substrate recognition or oligomerization both compromise CSR in splenic B cells. Collectively, our data implicate intrinsic preference of AID for structured substrates and uncover the importance of G4 recognition and oligomerization of AID in CSR.

  • Organizational Affiliation

    Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MBP fused activation-induced cytidine deaminaseA [auth B],
B [auth A]
549Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Mutation(s): 14 
Gene Names: malEZ5632ECs5017AICDAAID
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q9GZX7 (Homo sapiens)
Explore Q9GZX7 
Go to UniProtKB:  Q9GZX7
GTEx:  ENSG00000111732 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9Q9GZX7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.61 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.276 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.68α = 90
b = 167.65β = 90
c = 188.3γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description