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Yorodumi- PDB-6i04: Crystal structure of Sema domain of the Met receptor in complex w... -
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-Basic information
Entry | Database: PDB / ID: 6i04 | ||||||
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Title | Crystal structure of Sema domain of the Met receptor in complex with FAB | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MET / Sema domain | ||||||
Function / homology | Function and homology information hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / 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 ...hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / 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 / 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 / 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 / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. ...Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. / Logan, D.T. / Welin, M. / Chattopadhyay, S. / Harms, B.D. / Nielsen, U.B. / Schoeberl, B. / Lugovskoy, A.A. / MacBeath, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: MM-131, a bispecific anti-Met/EpCAM mAb, inhibits HGF-dependent and HGF-independent Met signaling through concurrent binding to EpCAM. Authors: Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. ...Authors: Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. / Logan, D.T. / Welin, M. / Chattopadhyay, S. / Harms, B.D. / Nielsen, U.B. / Schoeberl, B. / Lugovskoy, A.A. / MacBeath, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i04.cif.gz | 348.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i04.ent.gz | 275.2 KB | Display | PDB format |
PDBx/mmJSON format | 6i04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/6i04 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/6i04 | HTTPS FTP |
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-Related structure data
Related structure data | 6hygC 6i07C 4o3tS 4py7S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 62404.688 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): EXPI293F cells / Production host: Homo sapiens (human) References: UniProt: P08581, receptor protein-tyrosine kinase #2: Antibody | Mass: 24478.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293F cells / Production host: Homo sapiens (human) #3: Antibody | Mass: 23114.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293F cells / Production host: Homo sapiens (human) |
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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: 2.85 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18% w/v PEG 3350, 0.1 M ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→29.57 Å / Num. obs: 39528 / % possible obs: 96.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 71 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.169 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.1→3.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.033 / Mean I/σ(I) obs: 1 / Num. unique obs: 3994 / CC1/2: 0.446 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PY7, 4O3T Resolution: 3.1→29.56 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 29.744 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.497 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.843 Å2
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Refinement step | Cycle: 1 / Resolution: 3.1→29.56 Å
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Refine LS restraints |
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