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- PDB-1r1w: CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF THE HEPATOCYTE... -

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Basic information

Entry
Database: PDB / ID: 1r1w
TitleCRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF THE HEPATOCYTE GROWTH FACTOR RECEPTOR C-MET
ComponentsHEPATOCYTE GROWTH FACTOR RECEPTOR
KeywordsTRANSFERASE / RECEPTOR TYROSINE KINASE / SIGNAL TRANSDUCTION / GRB2 / SHC
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 / 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 ...negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor 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 / positive regulation of endothelial cell chemotaxis / negative regulation of stress fiber assembly / 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 / basal plasma membrane / molecular function activator activity / InlB-mediated entry of Listeria monocytogenes into host cell / excitatory postsynaptic potential / liver development / Negative regulation of MET activity / receptor protein-tyrosine kinase / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein phosphatase binding / cell surface receptor signaling pathway / receptor complex / postsynapse / 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 / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Resolution: 1.8 Å
AuthorsSchiering, N. / Knapp, S. / Marconi, M. / Flocco, M.M. / Cui, J. / Perego, R. / Rusconi, L. / Cristiani, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-Met and its complex with the microbial alkaloid K-252a
Authors: Schiering, N. / Knapp, S. / Marconi, M. / Flocco, M.M. / Cui, J. / Perego, R. / Rusconi, L. / Cristiani, C.
History
DepositionSep 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)35,3071
Polymers35,3071
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.038, 46.028, 158.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HEPATOCYTE GROWTH FACTOR RECEPTOR / MET PROTO-ONCOGENE TYROSINE KINASE / C-MET / HGF RECEPTOR / HGF-SF RECEPTOR


Mass: 35306.898 Da / Num. of mol.: 1 / Fragment: TYROSINE KINASE DOMAIN / Mutation: Y1194F, Y1234F, Y1235D, V1272L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Cell line (production host): HIGH-FIVE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08581, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: PEG 5000 MME, isopropanol, Hepes, pH 7.10, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris1droppH8.5
3150 mM1dropNaCl
410 %glycerol1drop
53 mMdithiothreitol1drop
66-10 %PEG5000 MME1reservoir
7100 mMHEPES1reservoirpH7.1
811 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 16, 2002
RadiationMonochromator: DIAMOND CYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 28705 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 19.6
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2644 / % possible all: 90.4
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 168428
Reflection shell
*PLUS
% possible obs: 90.4 %

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Processing

Software
NameVersionClassification
ProDCdata collection
SCALEPACKdata scaling
EPMRphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1r0p

1r0p


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.083 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: It is probable that HOH 1 is a chlorine. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20381 1405 4.9 %RANDOM
Rwork0.17297 ---
all0.17447 28705 --
obs0.17447 27250 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.291 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 0 233 2519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212338
X-RAY DIFFRACTIONr_bond_other_d0.0020.022171
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9533167
X-RAY DIFFRACTIONr_angle_other_deg0.80535044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5145283
X-RAY DIFFRACTIONr_chiral_restr0.0760.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022528
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02477
X-RAY DIFFRACTIONr_nbd_refined0.2440.2714
X-RAY DIFFRACTIONr_nbd_other0.2370.22472
X-RAY DIFFRACTIONr_nbtor_other0.0820.21234
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.23
X-RAY DIFFRACTIONr_mcbond_it0.6711.51428
X-RAY DIFFRACTIONr_mcangle_it1.27222318
X-RAY DIFFRACTIONr_scbond_it1.9593910
X-RAY DIFFRACTIONr_scangle_it3.2384.5849
LS refinement shellResolution: 1.8→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.221 94
Rwork0.189 1822
obs-1822
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.2038 / Rfactor Rwork: 0.1729
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.29

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