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Yorodumi- PDB-1shy: The Crystal Structure of HGF beta-chain in Complex with the Sema ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1shy | ||||||
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Title | The Crystal Structure of HGF beta-chain in Complex with the Sema Domain of the Met Receptor. | ||||||
Components |
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Keywords | GROWTH FACTOR/GROWTH FACTOR RECEPTOR / protease / sema domain / PSI domain / receptor ectodomain growth factor / GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins ...regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / semaphorin-plexin signaling pathway involved in axon guidance / hepatocyte growth factor receptor signaling pathway / semaphorin receptor activity / MET receptor recycling / semaphorin receptor complex / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / myoblast proliferation / Sema4D mediated inhibition of cell attachment and migration / MET activates PI3K/AKT signaling / negative regulation of stress fiber assembly / positive regulation of endothelial cell chemotaxis / negative regulation of Rho protein signal transduction / MET activates PTK2 signaling / cellular response to hepatocyte growth factor stimulus / positive regulation of DNA biosynthetic process / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of thrombin-activated receptor signaling pathway / 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 / semaphorin-plexin signaling pathway / epithelial to mesenchymal transition / establishment of skin barrier / positive regulation of osteoblast differentiation / MET activates RAS signaling / phagocytosis / MECP2 regulates neuronal receptors and channels / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of microtubule polymerization / Interleukin-7 signaling / negative regulation of autophagy / basal plasma membrane / cell chemotaxis / InlB-mediated entry of Listeria monocytogenes into host cell / platelet alpha granule lumen / liver development / epithelial cell proliferation / molecular function activator activity / growth factor activity / cell morphogenesis / neuron differentiation / Negative regulation of MET activity / receptor protein-tyrosine kinase / negative regulation of inflammatory response / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / Platelet degranulation / PIP3 activates AKT signaling / nervous system development / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / receptor complex / positive regulation of cell migration / positive regulation of protein phosphorylation / phosphorylation / signaling receptor binding / negative regulation of apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / 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: 3.22 Å | ||||||
Authors | Stamos, J. / Wiesmann, C. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Crystal structure of the HGF beta-chain in complex with the Sema domain of the Met receptor. Authors: Stamos, J. / Lazarus, R.A. / Yao, X. / Kirchhofer, D. / Wiesmann, C. #1: Journal: To be Published Title: Structural and functional basis of the serine protease-like HGF b-chain in Met binding and signaling Authors: Kirchhofer, D. / Xiaoyi, Y. / Peek, M. / Eigenbrot, C. / Lipari, M.T. / Billeci, K.L. / Maun, H.R. / Moran, P. / Santell, L. / Lazarus, R.A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED | ||||||
Remark 999 | SEQUENCE IN CHAIN B, THE FURIN CLEAVAGE SITE WAS REPLACED WITH A THROMBIN CLEAVAGE SITE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1shy.cif.gz | 156.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1shy.ent.gz | 121.8 KB | Display | PDB format |
PDBx/mmJSON format | 1shy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1shy_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 1shy_full_validation.pdf.gz | 476.9 KB | Display | |
Data in XML | 1shy_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 1shy_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/1shy ftp://data.pdbj.org/pub/pdb/validation_reports/sh/1shy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26014.117 Da / Num. of mol.: 1 / Fragment: HGF beta chain / Mutation: C604S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Production host: Escherichia coli (E. coli) / References: UniProt: P14210 |
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#2: Protein | Mass: 62535.852 Da / Num. of mol.: 1 / Fragment: Met receptor Sema and PSI domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08581 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.8 Å3/Da / Density % sol: 74.4 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.928 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 7, 2003 |
Radiation | Monochromator: monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 28312 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.058 |
Reflection shell | Resolution: 3.2→3.31 Å / Rsym value: 0.586 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HGF beta chain Resolution: 3.22→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.889 / SU B: 17.302 / SU ML: 0.297 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.83 / ESU R Free: 0.409
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.027 Å2
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Refinement step | Cycle: LAST / Resolution: 3.22→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.217→3.282 Å / Total num. of bins used: 25 /
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Refinement TLS params. | Method: refined / Origin x: -6.9404 Å / Origin y: 29.4231 Å / Origin z: 39.4854 Å
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Refinement TLS group |
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