[English] 日本語
Yorodumi- PDB-2uzx: Structure of the human receptor tyrosine kinase Met in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uzx | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein InlB: Crystal form I | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN/RECEPTOR / LEUCINE RICH REPEAT / RECEPTOR ECTODOMAIN / HEPATOCYTE GROWTH FACTOR RECEPTOR / SIGNALING PROTEIN / ATP-BINDING / TRANSFERASE / POLYMORPHISM / GLYCOPROTEIN / VIRULENCE FACTOR / DISEASE MUTATION / NUCLEOTIDE-BINDING / TRANSMEMBRANE / PROTO-ONCOGENE / PHOSPHORYLATION / LEUCINE-RICH REPEAT / ALTERNATIVE SPLICING / TYROSINE-PROTEIN KINASE / CHROMOSOMAL REARRANGEMENT / LRR / HGFR / KINASE / MEMBRANE / RECEPTOR / INTERNALIN / SIGNALING PROTEIN-RECEPTOR COMPLEX | ||||||
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 / 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 / cytoplasm Similarity search - Function | ||||||
Biological species | LISTERIA MONOCYTOGENES (bacteria) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Niemann, H.H. / Jager, V. / Butler, P.J.G. / Van Den Heuvel, J. / Schmidt, S. / Ferraris, D. / Gherardi, E. / Heinz, D.W. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2007 Title: Structure of the Human Receptor Tyrosine Kinase met in Complex with the Listeria Invasion Protein Inlb Authors: Niemann, H.H. / Jager, V. / Butler, P.J.G. / Van Den Heuvel, J. / Schmidt, S. / Ferraris, D. / Gherardi, E. / Heinz, D.W. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2uzx.cif.gz | 342.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2uzx.ent.gz | 271.9 KB | Display | PDB format |
PDBx/mmJSON format | 2uzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uzx ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uzx | HTTPS FTP |
---|
-Related structure data
Related structure data | 2uzyC 1h6tS 1shyS 1ux3S 2cewS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 32243.818 Da / Num. of mol.: 2 Fragment: INTERNALIN DOMAIN (CAP, LRR, IR), INLB321, RESIDUES 36-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Variant: SEROVAR 12A / Plasmid: PETM30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 CODONPLUS (DE3) / References: UniProt: P25147, UniProt: P0DQD2*PLUS #2: Protein | Mass: 81903.047 Da / Num. of mol.: 2 / Fragment: SEMA, PSI, IG1, MET741, RESIDUES 25-740 Source method: isolated from a genetically manipulated source Details: CONTAINS IG2 AND 6HIS TAG, WHICH ARE POORLY ORDERED AND NOT MODELED, MET WAS ENZYMATICALLY DEGLYCOSYLATED WITH ENDOH Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PA71D / Cell line (production host): CHO LEC 3.2.8.1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P08581 Compound details | MEDIATES THE ENTRY OF LISTERIA MONOCYTOGENES INTO CELLS. RECEPTOR FOR HEPATOCYTE GROWTH FACTOR AND ...MEDIATES THE ENTRY OF LISTERIA MONOCYTOGE | Sequence details | CHAIN A+C: RESIDUE 33-35 (GAM) REMAIN AFTER TEV CLEAVAGE CHAIN B+D: Y41C AND G344A PROBABLY DUE TO ...CHAIN A+C: RESIDUE 33-35 (GAM) REMAIN AFTER TEV CLEAVAGE CHAIN B+D: Y41C AND G344A PROBABLY DUE TO PCR ERROR. N-TERMINAL ETR LEFT AFTER PROCESSING | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 20 DEG C VAPOR DIFFUSION. 2 UL PROTEIN (5 MG/ML) PLUS 1 UL RESERVOIR CONSISTING OF 16.5% PEG 1500, 4.4% MPD, 0.1 M TRIS, PH8.5. RESERVOIR WAS COVERED WITH ALS OIL. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 51852 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 5.27 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.25 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.68 / % possible all: 79.9 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1H6T, 1SHY, 1UX3, 2CEW Resolution: 2.8→15 Å Details: B-FACTORS MODELED SOLELY BY TLS. TOTAL ISOTROPIC B-FACTORS GIVEN. TIGHT NCS ON INDIVIDUAL DOMAINS EMPLOYED THROUGHOUT REFINEMENT.
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
|