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- PDB-2uzx: Structure of the human receptor tyrosine kinase Met in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2uzx
TitleStructure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein InlB: Crystal form I
Components
  • HEPATOCYTE GROWTH FACTOR RECEPTOR
  • INTERNALIN B
KeywordsSIGNALING 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


negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET Receptor Activation / MET interacts with TNS proteins / endothelial cell morphogenesis / semaphorin receptor activity / MET receptor recycling / pancreas development ...negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET Receptor Activation / MET interacts with TNS proteins / endothelial cell morphogenesis / semaphorin receptor activity / 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 / positive regulation of endothelial cell chemotaxis / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of Rho protein signal transduction / negative regulation of thrombin-activated receptor signaling pathway / semaphorin-plexin signaling pathway / establishment of skin barrier / MET activates RAS signaling / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / negative regulation of autophagy / cell surface receptor protein tyrosine kinase signaling pathway / peptidoglycan-based cell wall / liver development / molecular function activator activity / InlB-mediated entry of Listeria monocytogenes into host cell / basal plasma membrane / excitatory postsynaptic potential / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / Negative regulation of MET activity / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / heparin binding / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / protein phosphatase binding / receptor complex / cell surface receptor signaling pathway / postsynapse / lipid binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal ...GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / Immunoglobulin-like - #1220 / : / Copper resistance protein CopC/internalin, immunoglobulin-like / Tyrosine-protein kinase, HGF/MSP receptor / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Leucine-rich repeat / 7 Propeller / Methylamine Dehydrogenase; Chain H / Leucine-rich repeat domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin E-set / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor receptor / Internalin B / Internalin B
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNiemann, H.H. / Jager, V. / Butler, P.J.G. / Van Den Heuvel, J. / Schmidt, S. / Ferraris, D. / Gherardi, E. / Heinz, D.W.
CitationJournal: 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
DepositionMay 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERNALIN B
B: HEPATOCYTE GROWTH FACTOR RECEPTOR
C: INTERNALIN B
D: HEPATOCYTE GROWTH FACTOR RECEPTOR


Theoretical massNumber of molelcules
Total (without water)228,2944
Polymers228,2944
Non-polymers00
Water00
1
A: INTERNALIN B
B: HEPATOCYTE GROWTH FACTOR RECEPTOR


Theoretical massNumber of molelcules
Total (without water)114,1472
Polymers114,1472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-7.2 kcal/mol
Surface area44590 Å2
MethodPQS
2
C: INTERNALIN B
D: HEPATOCYTE GROWTH FACTOR RECEPTOR


Theoretical massNumber of molelcules
Total (without water)114,1472
Polymers114,1472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-7.4 kcal/mol
Surface area44440 Å2
MethodPQS
Unit cell
Length a, b, c (Å)214.500, 66.700, 181.500
Angle α, β, γ (deg.)90.00, 123.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99868, -0.05125, 0.00388), (-0.05139, 0.99728, -0.05289), (-0.00116, -0.05302, -0.99859)56.01252, 3.11825, 74.68121
2given(-0.99933, -0.03665, -0.00066), (-0.03658, 0.99836, -0.04414), (0.00228, -0.04409, -0.99902)56.52769, 2.51149, 74.79391

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Components

#1: Protein INTERNALIN B / INLB


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 HEPATOCYTE GROWTH FACTOR RECEPTOR / HGF RECEPTOR / SCATTER FACTOR RECEPTOR / SF RECEPTOR / HGF/SF RECEPTOR / MET PROTO-ONCOGENE ...HGF RECEPTOR / SCATTER FACTOR RECEPTOR / SF RECEPTOR / HGF/SF RECEPTOR / MET PROTO-ONCOGENE TYROSINE KINASE / C-MET


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 detailsMEDIATES THE ENTRY OF LISTERIA MONOCYTOGENES INTO CELLS. RECEPTOR FOR HEPATOCYTE GROWTH FACTOR AND ...MEDIATES THE ENTRY OF LISTERIA MONOCYTOGENES INTO CELLS. RECEPTOR FOR HEPATOCYTE GROWTH FACTOR AND SCATTER FACTOR
Has protein modificationY
Sequence detailsCHAIN 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 OF IG-LEADER SEQUENCE. C-TERMINAL DLHHHHHH DUE TO CLONING AND HIS6 TAG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.8→2.9 Å / Redundancy: 3.25 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.68 / % possible all: 79.9

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1H6T, 1SHY, 1UX3, 2CEW

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.
RfactorNum. reflection% reflection
Rfree0.307 2471 5 %
Rwork0.268 --
obs-51852 96.9 %
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13170 0 0 0 13170

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