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Yorodumi- PDB-2qj4: A Mechanistic Basis for Converting a Receptor Tyrosine Kinase Ago... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qj4 | ||||||
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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 positive regulation of neuron projection regeneration / MET Receptor Activation / Drug-mediated inhibition of MET activation / MET interacts with TNS proteins / MET activates STAT3 / MET activates PI3K/AKT signaling / MET activates RAS signaling / MET activates PTPN11 / MET activates PTK2 signaling / MET activates RAP1 and RAC1 ...positive regulation of neuron projection regeneration / MET Receptor Activation / Drug-mediated inhibition of MET activation / MET interacts with TNS proteins / MET activates STAT3 / MET activates PI3K/AKT signaling / MET activates RAS signaling / MET activates PTPN11 / MET activates PTK2 signaling / MET activates RAP1 and RAC1 / MET receptor recycling / Negative regulation of MET activity / regulation of p38MAPK cascade / RAF/MAP kinase cascade / PIP3 activates AKT signaling / positive regulation of myelination / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Platelet degranulation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / hepatocyte growth factor receptor signaling pathway / myoblast proliferation / 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 / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / epithelial cell proliferation / cell chemotaxis / liver development / negative regulation of inflammatory response / growth factor activity / cell morphogenesis / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / 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 / protein-containing complex binding / proteolysis / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 2qj4.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qj4.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qj4_validation.pdf.gz | 451 KB | Display | wwPDB validaton report |
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Full document | 2qj4_full_validation.pdf.gz | 469.2 KB | Display | |
Data in XML | 2qj4_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 2qj4_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qj4 ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qj4 | HTTPS FTP |
-Related structure data
Related structure data | 2qj2C 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: 21208.139 Da / Num. of mol.: 2 / Fragment: residues 31-210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6J / Gene: Hgf / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE) / References: UniProt: Q08048 #2: Chemical | #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: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 mM ammonium sulfate, 26-32% PEG 1000, 50 mM Tris-HCl pH 8.0, 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: 1.00001 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 29, 2005 / 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: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→43.2 Å / Num. all: 13513 / Num. obs: 13513 / % possible obs: 75.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 2.37→2.45 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.2 / Num. unique all: 225 / Rsym value: 0.2 / % possible all: 12.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NK1 Resolution: 2.5→43.2 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 142016.27 / 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 using the least squares residual for twinning in CNS with a twin law of h,-h-k,-l, a twin fraction of 0.433, and ncs restraints between chain A and chain B.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.9365 Å2 / ksol: 0.380671 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→43.2 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
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Xplor file |
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