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Yorodumi- PDB-7ocm: K1K1H6, a potent recombinant minimal hepatocyte growth factor/sca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ocm | ||||||
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Title | K1K1H6, a potent recombinant minimal hepatocyte growth factor/scatter factor mimic | ||||||
Components | Hepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain | ||||||
Keywords | DE NOVO PROTEIN / MET receptor agonist / HGF/SF kringle 1 dimer / HGF/SF-derived recombinant protein / MET-activator / regeneration of epithelial tissue and organs / engineered 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: 1.7 Å | ||||||
Authors | de Jonge, H. / de Nola, G. / Gherardi, E. | ||||||
Citation | Journal: Life Sci Alliance / Year: 2022 Title: Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent MET receptor agonist. Authors: de Nola, G. / Leclercq, B. / Mougel, A. / Taront, S. / Simonneau, C. / Forneris, F. / Adriaenssens, E. / Drobecq, H. / Iamele, L. / Dubuquoy, L. / Melnyk, O. / Gherardi, E. / de Jonge, H. / Vicogne, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ocm.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ocm.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ocm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ocm_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 7ocm_full_validation.pdf.gz | 439.6 KB | Display | |
Data in XML | 7ocm_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 7ocm_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/7ocm ftp://data.pdbj.org/pub/pdb/validation_reports/oc/7ocm | HTTPS FTP |
-Related structure data
Related structure data | 7oclC 1bhtS 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
#1: Protein | Mass: 20061.537 Da / Num. of mol.: 1 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: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.16 % / Description: Thin hexagonal shaped |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM MOPS/HEPES pH 7.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 20% v/v glycerol, 10% w/v PEG4000 Temp details: Inside a fridge-like incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 29, 2014 / Details: Toroidal mirror | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.26→44.94 Å / Num. obs: 45262 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.041 / Rrim(I) all: 0.081 / Net I/σ(I): 8.4 / Num. measured all: 167746 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BHT Resolution: 1.7→35.89 Å / Cross valid method: THROUGHOUT
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||
Displacement parameters | Biso max: 67.43 Å2 / Biso mean: 22.03 Å2 / Biso min: 7.92 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35.89 Å
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LS refinement shell | Resolution: 1.7→1.79 Å
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