7O52

CD22 d6-d7 in complex with Fab m971


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.226 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural details of monoclonal antibody m971 recognition of the membrane-proximal domain of CD22.

Ereno-Orbea, J.Liu, X.Sicard, T.Kucharska, I.Li, W.Borovsky, D.Cui, H.Feng, Y.Dimitrov, D.S.Julien, J.P.

(2021) J Biol Chem 297: 100966-100966

  • DOI: https://doi.org/10.1016/j.jbc.2021.100966
  • Primary Citation of Related Structures:  
    7O4Y, 7O52

  • PubMed Abstract: 

    Cluster of differentiation-22 (CD22) belongs to the sialic acid-binding immunoglobulin (Ig)-like lectin family of receptors that is expressed on the surface of B cells. It has been classified as an inhibitory coreceptor for the B-cell receptor because of its function in establishing a baseline level of B-cell inhibition. The restricted expression of CD22 on B cells and its inhibitory function make it an attractive target for B-cell depletion in cases of B-cell malignancies. Genetically modified T cells with chimeric antigen receptors (CARs) derived from the m971 antibody have shown promise when used as an immunotherapeutic agent against B-cell acute lymphoblastic leukemia. A key aspect of the efficacy of this CAR-T was its ability to target a membrane-proximal epitope on the CD22 extracellular domain; however, the molecular details of m971 recognition of CD22 have thus far remained elusive. Here, we report the crystal structure of the m971 fragment antigen-binding in complex with the two most membrane-proximal Ig-like domains of CD22 (CD22 d6-d7 ). The m971 epitope on CD22 resides at the most proximal Ig domain (d7) to the membrane, and the antibody paratope contains electrostatic surfaces compatible with interactions with phospholipid head groups. Together, our data identify molecular details underlying the successful transformation of an antibody epitope on CD22 into an effective CAR immunotherapeutic target.


  • Organizational Affiliation

    Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada; Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
m971 Fab Heavy chainA [auth H]229Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
m971 Fab Light chainB [auth L]216Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CD22 d6-d7 Ig domainsC [auth U]194Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P20273 (Homo sapiens)
Explore P20273 
Go to UniProtKB:  P20273
PHAROS:  P20273
GTEx:  ENSG00000012124 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20273
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P20273-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth U]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth H],
E [auth H],
F [auth L],
J [auth U],
K [auth U]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth L],
H [auth L],
L [auth U]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.226 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.478α = 90
b = 119.719β = 90
c = 241.672γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary