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Yorodumi- PDB-1gp9: A New Crystal Form of the Nk1 Splice Variant of Hgf/Sf Demonstrat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gp9 | |||||||||
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Title | A New Crystal Form of the Nk1 Splice Variant of Hgf/Sf Demonstrates Extensive Hinge Movement and Suggests that the Nk1 Dimer Originates by Domain Swapping | |||||||||
Components | HEPATOCYTE GROWTH FACTOR | |||||||||
Keywords | HORMONE/GROWTH FACTOR / HGF/SF / NK1 / MET / DOMAIN SWAPPING / PROTEIN ENGINEERING / GROWTH FACTOR / KRINGLE / GLYCOPROTEIN / HORMONE-GROWTH FACTOR complex | |||||||||
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: 2.5 Å | |||||||||
Authors | Watanabe, K. / Chirgadze, D.Y. / Lietha, D. / Gherardi, E. / Blundell, T.L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: A New Crystal Form of the Nk1 Splice Variant of Hgf/Sf Demonstrates Extensive Hinge Movement and Suggests that the Nk1 Dimer Originates by Domain Swapping Authors: Watanabe, K. / Chirgadze, D.Y. / Lietha, D. / De Jonge, H. / Blundell, T.L. / Gherardi, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gp9.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gp9.ent.gz | 120.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gp9_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 1gp9_full_validation.pdf.gz | 518.6 KB | Display | |
Data in XML | 1gp9_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 1gp9_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gp9 ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gp9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20329.230 Da / Num. of mol.: 4 / Fragment: NK1, RESIDUES 40-210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: FIBROBLAST / Plasmid: PPIC-9K / Production host: Komagataella pastoris / Variant (production host): GS115 / References: UniProt: P14210 #2: Chemical | ChemComp-EPE / #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: 2.7 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 18% PEG4000, 10% 2-PROPANOL, 0.1M SODIUM HEPES, PH 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 3, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→30 Å / Num. obs: 33095 / % possible obs: 92.2 % / Observed criterion σ(I): 3 / Redundancy: 12.8 % / Biso Wilson estimate: 52.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.44→2.5 Å / Rmerge(I) obs: 0.352 / % possible all: 95.8 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS % possible obs: 95.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1NK1 1BHT Resolution: 2.5→19.92 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT / Bsol: 47.2027 Å2 / ksol: 0.319949 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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