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Yorodumi- PDB-2qj2: A Mechanistic Basis for Converting a Receptor Tyrosine Kinase Ago... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qj2 | ||||||
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Title | A Mechanistic Basis for Converting a Receptor Tyrosine Kinase Agonist to an Antagonist | ||||||
Components | Hepatocyte growth factor | ||||||
Keywords | HORMONE / HGF/SF / HORMONE/GROWTH FACTOR | ||||||
Function / homology | Function and homology information regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling ...regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling / MET activates PTPN11 / MET activates RAP1 and RAC1 / myoblast proliferation / MET activates PI3K/AKT signaling / MET activates PTK2 signaling / cellular response to hepatocyte growth factor stimulus / positive regulation of DNA biosynthetic process / chemoattractant activity / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / MET activates RAS signaling / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / epithelial cell proliferation / Interleukin-7 signaling / negative regulation of autophagy / cell chemotaxis / platelet alpha granule lumen / liver development / negative regulation of inflammatory response / growth factor activity / cell morphogenesis / Negative regulation of MET activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / Platelet degranulation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor binding / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Tolbert, W.D. / Daugherty, J. / Gao, C.-F. / Xe, Q. / Miranti, C. / Gherardi, E. / Vande Woude, G. / Xu, H.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist Authors: Tolbert, W.D. / Daugherty, J. / Gao, C. / Xie, Q. / Miranti, C. / Gherardi, E. / Vande Woude, G. / Xu, H.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qj2.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qj2.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qj2_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 2qj2_full_validation.pdf.gz | 458.2 KB | Display | |
Data in XML | 2qj2_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 2qj2_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qj2 ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qj2 | HTTPS FTP |
-Related structure data
Related structure data | 2qj4C 1nk1S 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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Details | The biological assembly is the dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 21159.236 Da / Num. of mol.: 2 / Fragment: residues 28-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE) / References: UniProt: P14210 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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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: 2.1 Å3/Da / Density % sol: 41.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 mM ammonium sulfate, 26-29% PEG 4000 (w/w), 100 mM Tris-HCl pH 8.0, 0.5 mM beta-octyl glucoside, and 5% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.99998 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 20, 2004 / Details: monochromator Si 1 1 1 |
Radiation | Monochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→22.3 Å / Num. all: 28061 / Num. obs: 28061 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1004 / Rsym value: 0.37 / % possible all: 31.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NK1 Resolution: 1.81→22.29 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 256166.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Refined to a maximum likelihood target using amplitudes.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.8867 Å2 / ksol: 0.446293 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.81→22.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.91 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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