+Open data
-Basic information
Entry | Database: PDB / ID: 4k24 | |||||||||
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Title | Structure of anti-uPAR Fab ATN-658 in complex with uPAR | |||||||||
Components |
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Keywords | IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information 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 / positive regulation of epidermal growth factor receptor signaling pathway / extracellular matrix structural constituent / cell adhesion mediated by integrin / polysaccharide binding / Syndecan interactions / extrinsic component of membrane / positive regulation of wound healing / plasminogen activation / 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 / positive regulation of DNA binding / 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 / fibrinolysis / collagen binding / extracellular matrix organization / cell-matrix adhesion / cell projection / Regulation of Complement cascade / liver regeneration / positive regulation of receptor-mediated endocytosis / Golgi lumen / chemotaxis / positive regulation of peptidyl-tyrosine phosphorylation / blood coagulation / cell migration / integrin binding / positive regulation of protein binding / signaling receptor activity / heparin binding / regulation of cell population proliferation / collagen-containing extracellular matrix / blood microparticle / cell adhesion / response to hypoxia / positive regulation of cell migration / positive regulation of protein phosphorylation / immune response / protein domain specific binding / endoplasmic reticulum lumen / external side of plasma membrane / intracellular membrane-bounded organelle / serine-type endopeptidase activity / focal adhesion / signaling receptor binding / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | |||||||||
Authors | Huang, M.D. / Xu, X. / Yuan, C. | |||||||||
Citation | Journal: Plos One / Year: 2014 Title: Identification of a New Epitope in uPAR as a Target for the Cancer Therapeutic Monoclonal Antibody ATN-658, a Structural Homolog of the uPAR Binding Integrin CD11b ( alpha M) Authors: Xu, X. / Cai, Y. / Wei, Y. / Donate, F. / Juarez, J. / Parry, G. / Chen, L. / Meehan, E.J. / Ahn, R.W. / Ugolkov, A. / Dubrovskyi, O. / O'halloran, T.V. / Huang, M. / Mazar, A.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k24.cif.gz | 373.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k24.ent.gz | 306.9 KB | Display | PDB format |
PDBx/mmJSON format | 4k24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k24_validation.pdf.gz | 968.9 KB | Display | wwPDB validaton report |
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Full document | 4k24_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4k24_validation.xml.gz | 59 KB | Display | |
Data in CIF | 4k24_validation.cif.gz | 77.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/4k24 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/4k24 | HTTPS FTP |
-Related structure data
Related structure data | 4k23SC 3bt2S 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
-Protein , 2 types, 2 molecules AU
#1: Protein | Mass: 15359.318 Da / Num. of mol.: 1 / Fragment: UNP residues 21-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: pMT/Bip / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 / References: UniProt: P00749, u-plasminogen activator |
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#5: Protein | Mass: 31601.479 Da / Num. of mol.: 1 / Fragment: UNP residues 23-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MO3, PLAUR, UPAR / Plasmid: pMT/Bip / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 / References: UniProt: Q03405 |
-Protein/peptide , 1 types, 1 molecules B
#2: Protein/peptide | Mass: 4573.103 Da / Num. of mol.: 1 / Fragment: UNP residues 21-60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VTN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04004 |
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-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 24482.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#4: Antibody | Mass: 24156.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Sugars , 3 types, 4 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-MAN / | #8: Sugar | ChemComp-NAG / | |
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-Details
Sequence details | A SEQUENCE DATABASE REFERENCE FOR ENTITY 3 AND 4 DOES NOT CURRENTLY EXIST. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.1 Å3/Da / Density % sol: 75.88 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 55%(v/v) Tacsimate, 2%(v/v) 2-methyl-1,3-propanediol, vapor diffusion, sitting drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.04 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 3, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.5→27 Å / Num. obs: 12451 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BT2(chain A, B, U), 4K23(chain H, L) Resolution: 4.5→26.902 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.51 / σ(F): 1.34 / Phase error: 30.96 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 284.9089 Å2
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Refinement step | Cycle: LAST / Resolution: 4.5→26.902 Å
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Refine LS restraints |
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LS refinement shell |
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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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