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Yorodumi- PDB-6gcu: MET receptor in complex with InlB internalin domain and DARPin A3A -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gcu | ||||||
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Title | MET receptor in complex with InlB internalin domain and DARPin A3A | ||||||
Components |
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Keywords | SIGNALING PROTEIN / receptor tyrosine kinase / bacterial invasion protein / artificial binding protein | ||||||
Function / homology | Function and homology information hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / entry of bacterium into host cell / Drug-mediated inhibition of MET activation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / semaphorin receptor activity ...hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / entry of bacterium into host cell / Drug-mediated inhibition of MET activation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / semaphorin receptor activity / positive regulation of endothelial cell chemotaxis / 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 / 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 / establishment of skin barrier / MET activates RAS signaling / phagocytosis / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / peptidoglycan-based cell wall / basal plasma membrane / negative regulation of autophagy / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / molecular function activator activity / Negative regulation of MET activity / receptor protein-tyrosine kinase / neuron differentiation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / heparin binding / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / cell surface receptor signaling pathway / receptor complex / phosphorylation / lipid binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Listeria monocytogenes serovar 1/2a (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.001 Å | ||||||
Authors | Meyer, T. / Andres, F. / Iamele, L. / Gherardi, E. / Pluckthun, A. / Niemann, H.H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Inhibition of the MET Kinase Activity and Cell Growth in MET-Addicted Cancer Cells by Bi-Paratopic Linking. Authors: Andres, F. / Iamele, L. / Meyer, T. / Stuber, J.C. / Kast, F. / Gherardi, E. / Niemann, H.H. / Pluckthun, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gcu.cif.gz | 442.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gcu.ent.gz | 352.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/6gcu ftp://data.pdbj.org/pub/pdb/validation_reports/gc/6gcu | HTTPS FTP |
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-Related structure data
Related structure data | 2uzyS S: Starting model for refinement |
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Similar 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: 81949.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Cell line (production host): CHO lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P08581, receptor protein-tyrosine kinase #2: Protein | Mass: 32243.818 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: inlB, lmo0434 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25147, UniProt: P0DQD3*PLUS #3: Protein | Mass: 18513.662 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria) |
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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: 2.94 Å3/Da / Density % sol: 58.2 % / Description: hexagonal, pointy-ended rods |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES sodium salt pH 7.5, 12% w/v PEG4000, protein complex concentration 5 mg/mL, equimolar ratio of macromolecules, drop size 0.2 uL, protein:reservoir ratio 1:1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9772 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9772 Å / Relative weight: 1 |
Reflection | Resolution: 6→48.15 Å / Num. obs: 7600 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 424 Å2 / CC1/2: 0.982 / R split: 0.136 / Rmerge(I) obs: 0.275 / Rpim(I) all: 0.107 / Rrim(I) all: 0.296 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 6→6.7 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.701 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2174 / CC1/2: 0.552 / Rpim(I) all: 0.646 / Rrim(I) all: 1.813 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UZY Resolution: 6.001→48.149 Å / SU ML: 0.95 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.62 Details: Rigid body and grouped B-factor refinement of the separate domains (SEMA, PSI, IPT1, IPT2, InlB321, DARPin A3A)
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 317.094 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.001→48.149 Å
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Refine LS restraints |
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LS refinement shell |
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