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

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Basic information

Entry
Database: PDB / ID: 2uzy
TitleStructure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein inlb: low resolution, Crystal form II
Components
  • HEPATOCYTE GROWTH FACTOR RECEPTORC-Met
  • INTERNALIN B
KeywordsSIGNALING PROTEIN/RECEPTOR / LEUCINE RICH REPEAT / RECEPTOR ECTODOMAIN / HEPATOCYTE GROWTH FACTOR RECEPTOR / 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 / 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
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 / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / 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 / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / ig-like, plexins, transcription factors / PSI domain / domain found in Plexins, Semaphorins and Integrins / Alpha-Beta Horseshoe / IPT domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / 7 Propeller / Methylamine Dehydrogenase; Chain H / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer 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: 4 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 1.3May 8, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation_author / exptl_crystal_grow ...citation_author / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation_author.name / _exptl_crystal_grow.method ..._citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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
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
Water0
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 area3180 Å2
ΔGint-9.4 kcal/mol
Surface area49230 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 area3150 Å2
ΔGint-8.4 kcal/mol
Surface area48350 Å2
MethodPQS
Unit cell
Length a, b, c (Å)139.000, 144.980, 150.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.978, 0.20856, 0.00355), (0.20859, 0.97789, 0.01507), (-0.00033, 0.01548, -0.99988)84.11283, -6.20879, -49.59385
2given(-0.96003, 0.27787, -0.03354), (0.27363, 0.957, 0.09632), (0.05886, 0.0833, -0.99478)86.70155, -11.59802, -49.28828
3given(-0.97779, 0.20349, -0.05021), (0.19959, 0.97714, 0.07322), (0.06396, 0.06158, -0.99605)85.03684, -6.81354, -50.48765
4given(-0.9778, 0.20953, 0.0024), (0.20953, 0.97751, 0.02397), (0.00268, 0.02394, -0.99971)84.42615, -6.45073, -49.37484
5given(-0.97989, 0.19755, -0.02815), (0.19582, 0.97911, 0.05473), (0.03838, 0.04811, -0.9981)84.28816, -6.57218, -48.53927

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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 36-321
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 / C-Met / 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, IG2\: MET741, RESIDUES 25-740
Source method: isolated from a genetically manipulated source
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
Sequence detailsCHAIN A+C: RESIDUES 33-35 (GAM) REMAIN AFTER TEV CLEAVAGE CHAIN B+D: Y41C AND G344A PROBABLY DUE TO ...CHAIN A+C: RESIDUES 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: 3

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: VAPOR DIFFUSION AT 25 DEGREE C IN SITTING-DROPS. 2 UL PROTEIN (8 MG/ML)PLUS 2 UL RESERVOIR (1.4 M NA/K PHOSPHATE, PH 6.5, 10% PEG 2000 MONO-METHYL-ETHER)

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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: 4→20 Å / Num. obs: 26274 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 5.99
Reflection shellResolution: 4→4.1 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.21 / % possible all: 99.9

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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

1h6t

1shy


Resolution: 4→15 Å
Details: B-FACTORS MODELED SOLELY BY TLS. TOTAL ISOTROPIC B-FACTORS GIVEN. TIGHT NCS ON INDIVIDUAL DOMAINS EMPLOYED THROUGHOUT.
RfactorNum. reflection% reflection
Rfree0.301 1286 5 %
Rwork0.251 --
obs-25699 97.55 %
Refinement stepCycle: LAST / Resolution: 4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14329 0 0 0 14329

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