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- PDB-3q6u: Structure of the apo MET receptor kinase in the dually-phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 3q6u
TitleStructure of the apo MET receptor kinase in the dually-phosphorylated, activated state
ComponentsHepatocyte growth factor receptor
KeywordsTRANSFERASE / tyrosine kinase
Function / homology
Function and homology information


negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor 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-plexin signaling pathway involved in axon guidance / semaphorin receptor activity ...negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor 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-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / MET receptor recycling / semaphorin receptor complex / 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 / 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 / negative regulation of autophagy / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / molecular function activator activity / neuron differentiation / Negative regulation of MET activity / receptor protein-tyrosine kinase / 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 / identical protein binding / membrane / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain ...Tyrosine-protein kinase, HGF/MSP receptor / 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSoisson, S.M. / Rickert, K.W. / Patel, S.B. / Allison, T. / Lumb, K.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis for selective small molecule kinase inhibition of activated c-Met.
Authors: Rickert, K.W. / Patel, S.B. / Allison, T.J. / Byrne, N.J. / Darke, P.L. / Ford, R.E. / Guerin, D.J. / Hall, D.L. / Kornienko, M. / Lu, J. / Munshi, S.K. / Reid, J.C. / Shipman, J.M. / ...Authors: Rickert, K.W. / Patel, S.B. / Allison, T.J. / Byrne, N.J. / Darke, P.L. / Ford, R.E. / Guerin, D.J. / Hall, D.L. / Kornienko, M. / Lu, J. / Munshi, S.K. / Reid, J.C. / Shipman, J.M. / Stanton, E.F. / Wilson, K.J. / Young, J.R. / Soisson, S.M. / Lumb, K.J.
History
DepositionJan 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hepatocyte growth factor receptor


Theoretical massNumber of molelcules
Total (without water)35,1271
Polymers35,1271
Non-polymers00
Water4,414245
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.720, 63.808, 112.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hepatocyte growth factor receptor / HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / ...HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / Tyrosine-protein kinase Met


Mass: 35126.641 Da / Num. of mol.: 1 / Fragment: residues 1048-1348, Kinase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21
References: UniProt: P08581, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15.6 mg/ml protein mixed in 1:1 ratio with reservoir containing 150 mM malic acid, 20% PEG3350., pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 2, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 50426 / Num. obs: 50426 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.058 / Χ2: 1.015 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.54.70.77845351.028188.8
1.5-1.565.60.65248321.025195.5
1.56-1.636.60.51150131.037198.1
1.63-1.727.10.39150050.98198.6
1.72-1.837.10.24650711.073198.8
1.83-1.977.20.14150721.03199.1
1.97-2.177.10.08550930.952199.2
2.17-2.487.10.06451721.046199.5
2.48-3.126.90.05351910.984199.3
3.12-506.60.03454421.006199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
BUSTER-TNTBUSTER-TNT 2.5.1refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→37.46 Å / Occupancy max: 1 / Occupancy min: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESTRAINT 1 : csdx_protgeo.dat (V1.40) 20080428 RESTRAINT 2 : nuclgeo.dat (V1.10) 20070206 RESTRAINT 3 : bcorrel.dat (V1.15) 20080423 RESTRAINT 4 : contact.dat (V1.15) 20070207 RESTRAINT 5 : ...Details: RESTRAINT 1 : csdx_protgeo.dat (V1.40) 20080428 RESTRAINT 2 : nuclgeo.dat (V1.10) 20070206 RESTRAINT 3 : bcorrel.dat (V1.15) 20080423 RESTRAINT 4 : contact.dat (V1.15) 20070207 RESTRAINT 5 : assume.dat (V1.8) 20070124 NCS MODEL : NONE TARGET RESTRAINT : NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1906 4.98 %RANDOM
Rwork0.1836 ---
all0.1851 38245 --
obs0.1851 38245 98.85 %-
Displacement parametersBiso max: 100.39 Å2 / Biso mean: 23.9084 Å2 / Biso min: 7.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.6951 Å20 Å20 Å2
2--0.9718 Å20 Å2
3---0.7233 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 0 245 2548
LS refinement shellResolution: 1.6→1.7 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2556 293 4.91 %
Rwork0.2116 5674 -
all0.2138 5967 -
obs--98.85 %

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