Crystal Structure of a Variant Human Activation-induced Deoxycytidine Deaminase as an MBP fusion protein

Experimental Data Snapshot

  • Resolution: 2.81 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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This is version 2.1 of the entry. See complete history


Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification.

Pham, P.Afif, S.A.Shimoda, M.Maeda, K.Sakaguchi, N.Pedersen, L.C.Goodman, M.F.

(2016) DNA Repair (Amst) 43: 48-56

  • DOI: https://doi.org/10.1016/j.dnarep.2016.05.029
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Activation-induced deoxycytidine deaminase (AID) initiates somatic hypermutation (SHM) and class-switch recombination (CSR) by deaminating C→U during transcription of Ig-variable (V) and Ig-switch (S) region DNA, which is essential to produce high-affinity antibodies. Here we report the crystal structure of a soluble human AID variant at 2.8Å resolution that favors targeting WRC motifs (W=A/T, R=A/G) in vitro, and executes Ig V SHM in Ramos B-cells. A specificity loop extending away from the active site to accommodate two purine bases next to C, differs significantly in sequence, length, and conformation from APOBEC proteins Apo3A and Apo3G, which strongly favor pyrimidines at -1 and -2 positions. Individual amino acid contributions to specificity and processivity were measured in relation to a proposed ssDNA binding cleft. This study provides a structural basis for residue contributions to DNA scanning properties unique to AID, and for disease mutations in human HIGM-2 syndrome.

  • Organizational Affiliation

    Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminaseA [auth C],
B [auth A],
C [auth B]
546Escherichia coli O157:H7Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEZ5632ECs5017AICDAAID
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZX7 (Homo sapiens)
Explore Q9GZX7 
Go to UniProtKB:  Q9GZX7
GTEx:  ENSG00000111732 
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Explore P0AEY0 
Go to UniProtKB:  P0AEY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9GZX7P0AEY0
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
D, E, F
Glycosylation Resources
GlyTouCan:  G87171PZ
GlyCosmos:  G87171PZ
GlyGen:  G87171PZ
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.81 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.793α = 90
b = 96.806β = 102.86
c = 108.692γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary