5W0R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


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Literature

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

  • 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 ...

    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. Electronic address: wu@crystal.harvard.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MBP fused activation-induced cytidine deaminaseB [auth A], A [auth B]549Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Mutation(s): 15 
Gene Names: malEZ5632ECs5017AICDAAID
EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZX7 (Homo sapiens)
Explore Q9GZX7 
Go to UniProtKB:  Q9GZX7
PHAROS:  Q9GZX7
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Explore P0AEY0 
Go to UniProtKB:  P0AEY0
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.96α = 90
b = 179.07β = 90
c = 188.08γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research InstituteUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release