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Yorodumi- PDB-3bt2: Structure of urokinase receptor, urokinase and vitronectin complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bt2 | |||||||||
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Title | Structure of urokinase receptor, urokinase and vitronectin complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / protein-protein interaction / Glycoprotein / GPI-anchor / Lipoprotein / Membrane / Receptor / Secreted / Blood coagulation / EGF-like domain / Fibrinolysis / Hydrolase / Kringle / Phosphoprotein / Plasminogen activation / Protease / Serine protease / Zymogen / Cell adhesion / Heparin-binding / Sulfation / Immunoglobulin domain | |||||||||
Function / homology | Function and homology information urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / rough endoplasmic reticulum lumen / smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of homotypic cell-cell adhesion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / alphav-beta3 integrin-vitronectin complex / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion ...urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / rough endoplasmic reticulum lumen / smooth muscle cell-matrix adhesion / peptidase inhibitor complex / positive regulation of homotypic cell-cell adhesion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / alphav-beta3 integrin-vitronectin complex / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / scavenger receptor activity / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / negative regulation of endopeptidase activity / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of proteolysis / negative regulation of plasminogen activation / negative regulation of blood coagulation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / serine-type endopeptidase complex / Dissolution of Fibrin Clot / positive regulation of cell-substrate adhesion / Molecules associated with elastic fibres / cell adhesion mediated by integrin / smooth muscle cell migration / extracellular matrix structural constituent / positive regulation of epidermal growth factor receptor signaling pathway / Syndecan interactions / polysaccharide binding / extrinsic component of membrane / positive regulation of wound healing / plasminogen activation / positive regulation of smooth muscle cell migration / oligodendrocyte differentiation / endodermal cell differentiation / tertiary granule membrane / regulation of cell adhesion mediated by integrin / positive regulation of release of cytochrome c from mitochondria / protein polymerization / basement membrane / ECM proteoglycans / positive regulation of DNA binding / Integrin cell surface interactions / negative regulation of fibrinolysis / negative regulation of intrinsic apoptotic signaling pathway / specific granule membrane / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / collagen binding / extracellular matrix organization / cell-matrix adhesion / cell projection / liver regeneration / Regulation of Complement cascade / Golgi lumen / positive regulation of receptor-mediated endocytosis / chemotaxis / cell migration / positive regulation of peptidyl-tyrosine phosphorylation / blood coagulation / integrin binding / signaling receptor activity / heparin binding / regulation of cell population proliferation / positive regulation of protein binding / collagen-containing extracellular matrix / blood microparticle / response to hypoxia / cell adhesion / positive regulation of cell migration / immune response / positive regulation of protein phosphorylation / protein domain specific binding / external side of plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / endoplasmic reticulum / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Huang, M. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes Authors: Huai, Q. / Zhou, A. / Lin, L. / Mazar, A.P. / Parry, G.C. / Callahan, J. / Shaw, D.E. / Furie, B. / Furie, B.C. / Huang, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bt2.cif.gz | 181.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bt2.ent.gz | 141.5 KB | Display | PDB format |
PDBx/mmJSON format | 3bt2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/3bt2 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/3bt2 | HTTPS FTP |
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-Related structure data
Related structure data | 3bt1C 2fd6S 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AU
#1: Protein | Mass: 15359.318 Da / Num. of mol.: 1 Fragment: urokinase amino terminal fragment, Urokinase-type plasminogen activator long chain A, UNP residues 21-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: pMT/Bip / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00749 |
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#5: Protein | Mass: 31601.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLAUR, MO3, UPAR / Plasmid: pMT/Bip / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells / References: UniProt: Q03405 |
-Antibody , 2 types, 2 molecules LH
#3: Antibody | Mass: 23269.691 Da / Num. of mol.: 1 / Fragment: Fab fragment, light chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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#4: Antibody | Mass: 23041.734 Da / Num. of mol.: 1 / Fragment: Fab fragment, heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
-Protein/peptide / Non-polymers , 2 types, 58 molecules B
#2: Protein/peptide | Mass: 4573.103 Da / Num. of mol.: 1 / Fragment: sometomedin-B domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VTN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04004 |
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#8: Water | ChemComp-HOH / |
-Sugars , 2 types, 3 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / | |
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-Details
Sequence details | THIS COORDINATES IN CHAINS L AND H ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. IT IS DUE TO KABAT-WU ...THIS COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.25 % |
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Crystal grow | Temperature: 295 K / Method: microdialysis / pH: 7.5 Details: 8% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 38381 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 24.1 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3675 / Rsym value: 0.356 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2fd6 Resolution: 2.5→42.88 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.878 / SU B: 28.105 / SU ML: 0.316 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.463 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.232 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→42.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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