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Yorodumi- PDB-3dsf: Crystal structure of anti-osteopontin antibody 23C3 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dsf | |||||||||
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Title | Crystal structure of anti-osteopontin antibody 23C3 in complex with W43A mutated epitope peptide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / osteopontin / OPN / antibody-antigen complex | |||||||||
Function / homology | Function and homology information negative regulation of collateral sprouting of intact axon in response to injury / positive regulation of estradiol secretion / androgen catabolic process / biomineral tissue development / response to macrophage colony-stimulating factor / Signaling by PDGF / cellular response to testosterone stimulus / response to vitamin D / RUNX3 Regulates Immune Response and Cell Migration / extracellular matrix binding ...negative regulation of collateral sprouting of intact axon in response to injury / positive regulation of estradiol secretion / androgen catabolic process / biomineral tissue development / response to macrophage colony-stimulating factor / Signaling by PDGF / cellular response to testosterone stimulus / response to vitamin D / RUNX3 Regulates Immune Response and Cell Migration / extracellular matrix binding / response to steroid hormone / small molecule binding / decidualization / positive regulation of bone resorption / Integrin cell surface interactions / Degradation of the extracellular matrix / embryo implantation / cell projection / cytokine activity / Post-translational protein phosphorylation / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / integrin binding / cell adhesion / endoplasmic reticulum lumen / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / extracellular space / extracellular exosome / extracellular region Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Du, J. / Zhong, C. / Yang, H. / Ding, J. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Molecular basis of recognition of human osteopontin by 23C3, a potential therapeutic antibody for treatment of rheumatoid arthritis Authors: Du, J. / Hou, S. / Zhong, C. / Lai, Z. / Yang, H. / Dai, J. / Zhang, D. / Wang, H. / Guo, Y. / Ding, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dsf.cif.gz | 165.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dsf.ent.gz | 129.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dsf_validation.pdf.gz | 743.9 KB | Display | wwPDB validaton report |
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Full document | 3dsf_full_validation.pdf.gz | 751.7 KB | Display | |
Data in XML | 3dsf_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 3dsf_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/3dsf ftp://data.pdbj.org/pub/pdb/validation_reports/ds/3dsf | HTTPS FTP |
-Related structure data
Related structure data | 3cxdSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23070.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: ascites |
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#2: Antibody | Mass: 23131.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: ascites |
#3: Protein/peptide | Mass: 1241.370 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: the peptide VATALNPDPSQK is synthesized at Shanghai HD Bioscience Company References: UniProt: P10451 |
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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-glucopyranose Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 0.2M di-ammonium hydrogen phosphate, 20% PEG3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 12159 / Num. obs: 12086 / % possible obs: 99.4 % / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.229 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CXD Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.83 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.454 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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