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Yorodumi- PDB-3hmr: Crystal structure of the N-terminal fragment (31-127) of the mous... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hmr | ||||||
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Title | Crystal structure of the N-terminal fragment (31-127) of the mouse hepatocyte growth factor/scatter factor | ||||||
Components | Hepatocyte growth factor | ||||||
Keywords | HORMONE / HGF/SF / hormone/growth factor / Disulfide bond / Glycoprotein / Growth factor / Kringle / Pyrrolidone carboxylic acid / Serine protease homolog | ||||||
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 / RAF/MAP kinase cascade / regulation of p38MAPK cascade / positive regulation of myelination / PIP3 activates AKT signaling / 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 / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / negative regulation of peptidyl-serine phosphorylation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cell chemotaxis / liver development / epithelial cell proliferation / growth factor activity / cell morphogenesis / negative regulation of inflammatory response / 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 / protein-containing complex binding / negative regulation of apoptotic process / 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 Å | ||||||
Authors | Tolbert, W.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural basis for agonism and antagonism of hepatocyte growth factor. Authors: Tolbert, W.D. / Daugherty-Holtrop, J. / 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 | 3hmr.cif.gz | 34.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hmr.ent.gz | 22.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/3hmr ftp://data.pdbj.org/pub/pdb/validation_reports/hm/3hmr | HTTPS FTP |
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-Related structure data
Related structure data | 3hmsC 3hmtC 3hn4C 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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-Components
#1: Protein | Mass: 11682.447 Da / Num. of mol.: 1 / Fragment: N-terminal domain: UNP residues 31-127 Source method: isolated from a genetically manipulated source Details: Expressed as a thioredoxin fusion protein / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hgf / Plasmid: pET-Duet1/Trx / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE) / References: UniProt: Q08048 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 mM Ammonium sulfate, 24-30% PEG 2000, 50 mM HEPES pH 8.0, 5% 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2006 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 8117 / Num. obs: 8117 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 7.7 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 1.7 / Num. unique all: 877 / Rsym value: 0.415 / % possible all: 53.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NK1 Resolution: 2→39.82 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 80574.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.1047 Å2 / ksol: 0.395291 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→39.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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