[English] 日本語
Yorodumi- PDB-1r0p: Crystal structure of the tyrosine kinase domain of the hepatocyte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r0p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-Met in complex with the microbial alkaloid K-252a | ||||||
Components | Hepatocyte growth factor receptor | ||||||
Keywords | TRANSFERASE / Receptor tyrosine kinase / Signal Transduction / Grb2 / Shc | ||||||
Function / homology | Function and homology information hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / endothelial cell morphogenesis / semaphorin receptor activity / MET receptor recycling ...hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / endothelial cell morphogenesis / semaphorin receptor activity / MET receptor recycling / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / MET activates PI3K/AKT signaling / positive regulation of endothelial cell chemotaxis / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of thrombin-activated receptor signaling pathway / semaphorin-plexin signaling pathway / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / establishment of skin barrier / MET activates RAS signaling / phagocytosis / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / negative regulation of autophagy / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / excitatory postsynaptic potential / molecular function activator activity / receptor protein-tyrosine kinase / Negative regulation of MET activity / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein phosphatase binding / postsynapse / receptor complex / cell surface receptor signaling pathway / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Schiering, N. / Knapp, S. / Marconi, M. / Flocco, M.M. / Cui, J. / Perego, R. / Rusconi, L. / Cristiani, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-Met and its complex with the microbial alkaloid K-252a Authors: Schiering, N. / Knapp, S. / Marconi, M. / Flocco, M.M. / Cui, J. / Perego, R. / Rusconi, L. / Cristiani, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1r0p.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1r0p.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 1r0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r0p_validation.pdf.gz | 462.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1r0p_full_validation.pdf.gz | 465.7 KB | Display | |
Data in XML | 1r0p_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 1r0p_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/1r0p ftp://data.pdbj.org/pub/pdb/validation_reports/r0/1r0p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35306.898 Da / Num. of mol.: 1 / Fragment: tyrosine kinase domain / Mutation: Y1194F, Y1234F, Y1235D, V1272L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Cell line (production host): High-five / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08581, EC: 2.7.1.112 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: PEG 5000 MME, isopropanol, Hepes, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 16, 2002 |
Radiation | Monochromator: diamond cystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 29021 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 34 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 12.2 / Num. unique all: 2638 / % possible all: 89.2 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 144096 |
Reflection shell | *PLUS % possible obs: 89.2 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.033 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 12.236 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Num. reflection obs: 27533 / Rfactor Rfree: 0.1973 / Rfactor Rwork: 0.1695 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|