5W0U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  5W0R, 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
B, A
549Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Gene Names: malE, AICDA (AID)
EC: 3.5.4.38
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AEY0
Find proteins for Q9GZX7 (Homo sapiens)
Go to Gene View: AICDA
Go to UniProtKB:  Q9GZX7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3')D12Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3')G12Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCM
Query on DCM

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A, B
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O7 P
NCMVOABPESMRCP-SHYZEUOFSA-N
 Ligand Interaction
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.251 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.005α = 90.00
b = 39.777β = 90.14
c = 153.935γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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