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- PDB-9rob: Crystal structure of human CD22 Ig domains 1-3 in complex with mo... -

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Basic information

Entry
Database: PDB / ID: 9rob
TitleCrystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 1B
ComponentsB-cell receptor CD22
KeywordsIMMUNE SYSTEM / Siglec / sialic acid / B cell
Function / homology
Function and homology information


regulation of B cell proliferation / IgM binding / negative regulation of immunoglobulin production / negative regulation of B cell receptor signaling pathway / sialic acid binding / CD22 mediated BCR regulation / negative regulation of calcium-mediated signaling / CD4 receptor binding / neuronal cell body membrane / regulation of endocytosis ...regulation of B cell proliferation / IgM binding / negative regulation of immunoglobulin production / negative regulation of B cell receptor signaling pathway / sialic acid binding / CD22 mediated BCR regulation / negative regulation of calcium-mediated signaling / CD4 receptor binding / neuronal cell body membrane / regulation of endocytosis / B cell activation / regulation of immune response / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / recycling endosome / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / carbohydrate binding / protein phosphatase binding / early endosome / cell adhesion / signaling receptor binding / external side of plasma membrane / cell surface / extracellular exosome / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / B-cell receptor CD22-like, first Ig-like / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin ...: / B-cell receptor CD22-like, first Ig-like / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / B-cell receptor CD22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEreno-Orbea, J. / Sicard, T. / Julien, J.-P.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)BPF-144483 Canada
Canadian Institutes of Health Research (CIHR)PJT-148811 Canada
CitationJournal: Jacs Au / Year: 2025
Title: Molecular Insights into the Engagement of High-Affinity Sialylated Ligands to Human CD22.
Authors: Ereno-Orbea, J. / Pang, L. / Sicard, T. / Nycholat, C. / Cui, H. / Borovsky, D. / Franconetti, A. / Jimenez-Barbero, J. / Paulson, J.C. / Julien, J.P.
History
DepositionJun 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-cell receptor CD22
B: B-cell receptor CD22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0659
Polymers73,3212
Non-polymers2,7447
Water34219
1
A: B-cell receptor CD22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9864
Polymers36,6601
Non-polymers1,3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B-cell receptor CD22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0795
Polymers36,6601
Non-polymers1,4184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.621, 111.099, 164.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein B-cell receptor CD22 / B-lymphocyte cell adhesion molecule / BL-CAM / Sialic acid-binding Ig-like lectin 2 / Siglec-2 / T- ...B-lymphocyte cell adhesion molecule / BL-CAM / Sialic acid-binding Ig-like lectin 2 / Siglec-2 / T-cell surface antigen Leu-14


Mass: 36660.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD22, SIGLEC2 / Production host: Homo sapiens (human) / References: UniProt: P20273
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-A1JJN / (2R,4S,5R,6R)-5-acetamido-2-[[2,3-bis(chloranyl)phenyl]methoxy]-6-[(1R,2R)-1,2-bis(oxidanyl)-3-[(4-phenylphenyl)carbonylamino]propyl]-4-oxidanyl-oxane-2-carboxylic acid


Mass: 647.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H32Cl2N2O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 4000, 0.6 M NaCl, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97851 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 2.7→41.01 Å / Num. obs: 23446 / % possible obs: 99.9 % / Redundancy: 12.03 % / CC1/2: 0.99 / Net I/σ(I): 19.62
Reflection shellResolution: 2.7→2.86 Å / Num. unique obs: 3716 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIXv1.13refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→41.01 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2674 -5 %
Rwork0.2212 --
obs0.2235 23394 100 %
Refinement stepCycle: LAST / Resolution: 2.7→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 184 19 4979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.56
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.82290.32761450.28772743X-RAY DIFFRACTION100
2.8229-2.97160.3661440.28692737X-RAY DIFFRACTION100
2.9716-3.15780.31961440.2732743X-RAY DIFFRACTION100
3.1578-3.40150.30481450.2662747X-RAY DIFFRACTION100
3.4015-3.74360.27231450.23662753X-RAY DIFFRACTION100
3.7436-4.28480.25751460.20462781X-RAY DIFFRACTION100
4.2848-5.39640.20691480.17962805X-RAY DIFFRACTION100
5.3964-41.010.26091530.20212915X-RAY DIFFRACTION100

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