9ROB | pdb_00009rob

Crystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 1B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.267 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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Literature

Molecular Insights into the Engagement of High-Affinity Sialylated Ligands to Human CD22.

Ereno-Orbea, J.Pang, L.Sicard, T.Nycholat, C.Cui, H.Borovsky, D.Franconetti, A.Jimenez-Barbero, J.Paulson, J.C.Julien, J.P.

(2025) JACS Au 5: 5524-5537

  • DOI: https://doi.org/10.1021/jacsau.5c01013
  • Primary Citation of Related Structures:  
    9RO7, 9ROB

  • PubMed Abstract: 

    CD22 is a sialic acid-binding immunoglobulin-like lectin (Siglec) that maintains a baseline level of B cell inhibition. Its function and restricted expression in B cells make CD22 a validated target in therapies against dysregulated B cells, which cause cancer and autoimmune diseases. High-affinity sialic acid-based ligands capable of competing with natural ligands to bind CD22 represent a promising therapeutic opportunity. Here, we describe the design and synthesis of a sialoside library constructed by chemical modifications on carbon C2 of 9- N -biphenylcarboxamide Neu5Ac ( BPC Neu5Ac) or 9- N -m-phenoxybenzamide Neu5FAc ( MPB Neu5FAc) scaffold using a copper-(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. Subsequent analysis of binding to human CD22 using competitive binding assays and isothermal titration calorimetry reveals that addition of noncarbohydrate substituents at C2 and C9 can improve the affinity toward CD22 from high micromolar to submicromolar K D values. We describe the molecular basis of this affinity improvement for three of the newly synthesized compounds by solving cocrystal structures in complex with CD22. These findings contribute to our understanding of the affinity increase of chemically modified Neu5Ac toward CD22, providing the molecular basis for further compound design of sialic acid-based molecules with potential therapeutic relevance.


  • Organizational Affiliation
    • Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell receptor CD22
A, B
324Homo sapiensMutation(s): 5 
Gene Names: CD22SIGLEC2
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
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth D],
D [auth H]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.621α = 90
b = 111.099β = 90
c = 164.282γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaBPF-144483
Canadian Institutes of Health Research (CIHR)CanadaPJT-148811

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release