+Open data
-Basic information
Entry | Database: PDB / ID: 5vkj | |||||||||
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Title | Crystal structure of human CD22 Ig domains 1-3 | |||||||||
Components | B-cell receptor CD22 | |||||||||
Keywords | IMMUNE SYSTEM / Siglec / Sialic acid / carbohydrate binding protein | |||||||||
Function / homology | Function and homology information regulation of B cell proliferation / negative regulation of B cell receptor signaling pathway / IgM binding / negative regulation of immunoglobulin production / negative regulation of calcium-mediated signaling / sialic acid binding / CD22 mediated BCR regulation / CD4 receptor binding / neuronal cell body membrane / B cell activation ...regulation of B cell proliferation / negative regulation of B cell receptor signaling pathway / IgM binding / negative regulation of immunoglobulin production / negative regulation of calcium-mediated signaling / sialic acid binding / CD22 mediated BCR regulation / CD4 receptor binding / neuronal cell body membrane / B cell activation / regulation of endocytosis / 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 / external side of plasma membrane / signaling receptor binding / cell surface / extracellular exosome / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | |||||||||
Authors | Julien, J.P. / Ereno-Orbea, J. / Sicard, T. | |||||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Molecular basis of human CD22 function and therapeutic targeting. Authors: June Ereño-Orbea / Taylor Sicard / Hong Cui / Mohammad T Mazhab-Jafari / Samir Benlekbir / Alba Guarné / John L Rubinstein / Jean-Philippe Julien / 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 ...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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vkj.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vkj.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vkj_validation.pdf.gz | 785.7 KB | Display | wwPDB validaton report |
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Full document | 5vkj_full_validation.pdf.gz | 785.9 KB | Display | |
Data in XML | 5vkj_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 5vkj_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/5vkj ftp://data.pdbj.org/pub/pdb/validation_reports/vk/5vkj | HTTPS FTP |
-Related structure data
Related structure data | 8704C 8705C 5vkkC 5vkmC 5vl3C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | Monomer as determined by gel filtration |
-Components
#1: Protein | Mass: 36660.293 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 20-330 / Mutation: N67A,N112A,N135A,N164A,N231A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD22, SIGLEC2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P20273 | ||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 30% PEG 4000, 0.2 M lithium chloride and 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→46.242 Å / Num. obs: 18725 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.12→2.2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.4571 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1848 / CC1/2: 0.801 / Rpim(I) all: 0.229 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Crystal structure from a different crystal obtained with this construct by MAD phasing with heavy atom Resolution: 2.12→46.242 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→46.242 Å
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Refine LS restraints |
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LS refinement shell |
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