5VL3

CD22 d1-d3 in complex with therapeutic Fab Epratuzumab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis of human CD22 function and therapeutic targeting.

Ereno-Orbea, J.Sicard, T.Cui, H.Mazhab-Jafari, M.T.Benlekbir, S.Guarne, A.Rubinstein, J.L.Julien, J.P.

(2017) Nat Commun 8: 764-764

  • DOI: 10.1038/s41467-017-00836-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CD22 maintains a baseline level of B-cell inhibition to keep humoral immunity in check. As a B-cell-restricted antigen, CD22 is targeted in therapies against dysregulated B cells that cause autoimmune diseases and blood cancers. Here we report the cr ...

    CD22 maintains a baseline level of B-cell inhibition to keep humoral immunity in check. As a B-cell-restricted antigen, CD22 is targeted in therapies against dysregulated B cells that cause autoimmune diseases and blood cancers. Here we report the crystal structure of human CD22 at 2.1 Å resolution, which reveals that specificity for α2-6 sialic acid ligands is dictated by a pre-formed β-hairpin as a unique mode of recognition across sialic acid-binding immunoglobulin-type lectins. The CD22 ectodomain adopts an extended conformation that facilitates concomitant CD22 nanocluster formation on B cells and binding to trans ligands to avert autoimmunity in mammals. We structurally delineate the CD22 site targeted by the therapeutic antibody epratuzumab at 3.1 Å resolution and determine a critical role for CD22 N-linked glycosylation in antibody engagement. Our studies provide molecular insights into mechanisms governing B-cell inhibition and valuable clues for the design of immune modulators in B-cell dysfunction.The B-cell-specific co-receptor CD22 is a therapeutic target for depleting dysregulated B cells. Here the authors structurally characterize the ectodomain of CD22 and present its crystal structure with the bound therapeutic antibody epratuzumab, which gives insights into the mechanism of inhibition of B-cell activation.


    Organizational Affiliation

    Department of Immunology, University of Toronto, Toronto, ON, Canada, M5S 1A8. jean-philippe.julien@sickkids.ca.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada, M5G 0A4. jean-philippe.julien@sickkids.ca.,Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON, Canada, L8S 4L8.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada, M5G 0A4.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada, M5G 1L7.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8. jean-philippe.julien@sickkids.ca.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
B-cell receptor CD22
Q, R, S, T
323Homo sapiensMutation(s): 4 
Gene Names: CD22 (SIGLEC2)
Find proteins for P20273 (Homo sapiens)
Go to Gene View: CD22
Go to UniProtKB:  P20273
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Epratuzumab Fab Heavy Chain
A, C, E, H
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Epratuzumab Fab Light Chain
B, D, F, L
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
Q, R, T
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
Q, R, S, T
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
Q, R, S, T
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.280 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 87.110α = 70.83
b = 90.220β = 80.81
c = 136.632γ = 80.99
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XPREPdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaPJT-148811
Canadian Institutes of Health ResearchCanadaBPF-144483
Canadian Institutes of Health ResearchCanadaCanada Graduate Scholarship Masters Award

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references