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- PDB-9ro7: Crystal structure of human CD22 Ig domains 1-3 in complex with mo... -

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Basic information

Entry
Database: PDB / ID: 9ro7
TitleCrystal structure of human CD22 Ig domains 1-3 in complex with modified sialoside 7-012
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: 3.15 Å
AuthorsEreno-Orbea, J. / Sicard, T. / Julien, J.-P.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)BPF-14448 Canada
Canadian Institutes of Health Research (CIHR)PJT-14881 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
C: B-cell receptor CD22
D: B-cell receptor CD22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,41517
Polymers146,6414
Non-polymers5,77313
Water00
1
A: B-cell receptor CD22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0804
Polymers36,6601
Non-polymers1,4193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B-cell receptor CD22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0804
Polymers36,6601
Non-polymers1,4193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: B-cell receptor CD22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1765
Polymers36,6601
Non-polymers1,5154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: B-cell receptor CD22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0804
Polymers36,6601
Non-polymers1,4193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.395, 113.294, 138.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4
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.: 4 / Source method: obtained synthetically
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-A1JJO / (2R,4S,5R,6R)-5-acetamido-6-[(1S,2S)-1,2-bis(oxidanyl)-3-[(4-phenylphenyl)carbonylamino]propyl]-2-[[1-[(2R)-3-(2-methyl-5-nitro-imidazol-1-yl)-2-oxidanyl-propyl]-1,2,3-triazol-4-yl]methyl]-4-oxidanyl-oxane-2-carboxylic acid


Mass: 736.728 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H40N8O11 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.15→39.425 Å / Num. obs: 28599 / % possible obs: 99.4 % / Redundancy: 5.897 % / CC1/2: 0.99 / Net I/σ(I): 7.7
Reflection shellResolution: 3.15→3.32 Å / Num. unique obs: 4415 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→39.425 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2977 1422 5 %
Rwork0.2391 --
obs0.242 28430 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→39.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9490 0 393 0 9883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410150
X-RAY DIFFRACTIONf_angle_d0.70913827
X-RAY DIFFRACTIONf_dihedral_angle_d9.1966167
X-RAY DIFFRACTIONf_chiral_restr0.0421564
X-RAY DIFFRACTIONf_plane_restr0.0041839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1501-3.26260.43621390.34832645X-RAY DIFFRACTION100
3.2626-3.39320.37661390.32042659X-RAY DIFFRACTION100
3.3932-3.54750.31541410.28282687X-RAY DIFFRACTION100
3.5475-3.73440.33431390.25922640X-RAY DIFFRACTION100
3.7344-3.96820.30081410.24792686X-RAY DIFFRACTION100
3.9682-4.27420.27321420.21312683X-RAY DIFFRACTION100
4.2742-4.70370.25221410.20082701X-RAY DIFFRACTION100
4.7037-5.38290.27251440.20792715X-RAY DIFFRACTION100
5.3829-6.77630.30181440.23752731X-RAY DIFFRACTION100
6.7763-39.4250.26641520.21582861X-RAY DIFFRACTION100

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