5VL3

CD22 d1-d3 in complex with therapeutic Fab Epratuzumab

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.281 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: https://doi.org/10.1038/s41467-017-00836-6
  • Primary Citation of Related Structures:  
    5VKJ, 5VKK, 5VKM, 5VL3

  • 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 crystal structure of human CD22 at 2 ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
B-cell receptor CD22A [auth Q],
B [auth R],
C [auth S],
D [auth T]		323Homo sapiensMutation(s): 4 
Gene Names: CD22, SIGLEC2
UniProt & NIH Common Fund Data Resources
Find proteins for P20273 (Homo sapiens)
Explore P20273 
Go to UniProtKB:  P20273
PHAROS:  P20273
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20273
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Epratuzumab Fab Heavy ChainE [auth A],
F [auth C],
G [auth E],
H		222Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
UniProt
Find proteins for S6B291 (Homo sapiens)
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Go to UniProtKB:  S6B291
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UniProt GroupS6B291
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Epratuzumab Fab Light ChainI [auth B],
J [auth D],
K [auth F],
L		222Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
UniProt
Find proteins for Q8TCD0 (Homo sapiens)
Explore Q8TCD0 
Go to UniProtKB:  Q8TCD0
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UniProt GroupQ8TCD0
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth G],
O [auth J],
Q [auth M],
S [auth O]		2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth I]5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseP [auth K],
T [auth P]		4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseR [auth N]3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
U [auth S]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.281 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.11α = 70.83
b = 90.22β = 80.81
c = 136.632γ = 80.99
Software Package:
Software NamePurpose
PHENIXrefinement
XPREPdata scaling
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)CanadaPJT-148811
Canadian Institutes of Health Research (CIHR)CanadaBPF-144483
Canadian Institutes of Health Research (CIHR)CanadaCanada Graduate Scholarship Masters Award

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary