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- PDB-3bt2: Structure of urokinase receptor, urokinase and vitronectin complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bt2 | |||||||||
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Title | Structure of urokinase receptor, urokinase and vitronectin complex | |||||||||
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![]() | 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 | ![]() urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / 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 / smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / 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 / smooth muscle cell migration / cell adhesion mediated by integrin / positive regulation of epidermal growth factor receptor signaling pathway / extracellular matrix structural constituent / Syndecan interactions / polysaccharide binding / positive regulation of wound healing / extrinsic component of membrane / plasminogen activation / positive regulation of DNA binding / positive regulation of smooth muscle cell migration / endodermal cell differentiation / oligodendrocyte differentiation / positive regulation of release of cytochrome c from mitochondria / regulation of cell adhesion mediated by integrin / tertiary granule membrane / basement membrane / protein polymerization / ECM proteoglycans / Integrin cell surface interactions / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / negative regulation of intrinsic apoptotic signaling pathway / serine protease inhibitor complex / collagen binding / fibrinolysis / extracellular matrix organization / cell-matrix adhesion / Regulation of Complement cascade / cell projection / liver regeneration / positive regulation of receptor-mediated endocytosis / Golgi lumen / positive regulation of peptidyl-tyrosine phosphorylation / chemotaxis / blood coagulation / integrin binding / cell migration / positive regulation of protein binding / signaling receptor activity / heparin binding / regulation of cell population proliferation / 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 / endoplasmic reticulum lumen / external side of plasma membrane / intracellular membrane-bounded organelle / serine-type endopeptidase activity / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / signal transduction / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, M. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.8 KB | Display | ![]() |
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PDB format | ![]() | 141.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bt1C ![]() 2fd6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
-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.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
-Protein/peptide / Non-polymers , 2 types, 58 molecules B![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#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.) ![]() ![]() ![]() |
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#8: Water | ChemComp-HOH / |
-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#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: ![]() |
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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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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