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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 RECEPTORC-Met
  • 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


hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of guanyl-nucleotide exchange factor activity / MET interacts with TNS proteins / MET Receptor Activation / positive regulation of endothelial cell chemotaxis / semaphorin receptor activity ...hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of guanyl-nucleotide exchange factor activity / MET interacts with TNS proteins / MET Receptor Activation / positive regulation of endothelial cell chemotaxis / semaphorin receptor activity / Sema4D mediated inhibition of cell attachment and migration / MET receptor recycling / pancreas development / MET activates PTPN11 / negative regulation of Rho protein signal transduction / MET activates PI3K/AKT signaling / MET activates RAP1 and RAC1 / negative regulation of stress fiber assembly / negative regulation of thrombin-activated receptor signaling pathway / semaphorin-plexin signaling pathway / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / establishment of skin barrier / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / MET activates RAS signaling / phagocytosis / negative regulation of autophagy / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / Negative regulation of MET activity / neuron differentiation / receptor protein-tyrosine kinase / transmembrane receptor protein tyrosine kinase activity / positive regulation of kinase activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / nervous system development / transmembrane receptor protein tyrosine kinase signaling pathway / cell migration / heparin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of protein kinase B signaling / protein phosphatase binding / cell surface receptor signaling pathway / receptor complex / lipid binding / cell surface / signal transduction / plasma membrane => GO:0005886 / positive regulation of transcription by RNA polymerase II / extracellular region / membrane => GO:0016020 / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Listeria-Bacteroides repeat domain (List_Bact_rpt) / Listeria-Bacteroides repeat domain superfamily / Listeria/Bacterioides repeat / Leucine-rich repeat-containing adjacent domain / LRR adjacent / GW (Gly-Tryp) dipeptide domain / GW domain / GW domain profile. / GW domain superfamily / Internalin, N-terminal ...Listeria-Bacteroides repeat domain (List_Bact_rpt) / Listeria-Bacteroides repeat domain superfamily / Listeria/Bacterioides repeat / Leucine-rich repeat-containing adjacent domain / LRR adjacent / GW (Gly-Tryp) dipeptide domain / GW domain / GW domain profile. / GW domain superfamily / 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 superfamily / Sema domain / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / domain found in Plexins, Semaphorins and Integrins / PSI domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / IPT domain / Alpha-Beta Horseshoe / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine rich repeat / YVTN repeat-like/Quinoprotein amine dehydrogenase / Leucine-rich repeat profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor receptor / Internalin B / Internalin B
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (unknown)
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
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

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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 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 (unknown) / 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, 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
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
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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