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- PDB-2qj2: A Mechanistic Basis for Converting a Receptor Tyrosine Kinase Ago... -

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Basic information

Entry
Database: PDB / ID: 2qj2
TitleA Mechanistic Basis for Converting a Receptor Tyrosine Kinase Agonist to an Antagonist
ComponentsHepatocyte growth factor
KeywordsHORMONE / HGF/SF / HORMONE/GROWTH FACTOR
Function / homology
Function and homology information


positive regulation of neuron projection regeneration / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / regulation of p38MAPK cascade / Drug-mediated inhibition of MET activation / MET activates STAT3 / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of myelination / MET interacts with TNS proteins / regulation of tau-protein kinase activity ...positive regulation of neuron projection regeneration / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / regulation of p38MAPK cascade / Drug-mediated inhibition of MET activation / MET activates STAT3 / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of myelination / MET interacts with TNS proteins / regulation of tau-protein kinase activity / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling / MET activates PTPN11 / MET activates RAP1 and RAC1 / MET activates PI3K/AKT signaling / myoblast proliferation / positive regulation of DNA biosynthetic process / MET activates PTK2 signaling / cellular response to hepatocyte growth factor stimulus / positive regulation of interleukin-10 production / negative regulation of release of cytochrome c from mitochondria / negative regulation of interleukin-6 production / epithelial to mesenchymal transition / chemoattractant activity / positive regulation of osteoblast differentiation / MET activates RAS signaling / animal organ regeneration / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of peptidyl-serine phosphorylation / Interleukin-7 signaling / cell chemotaxis / negative regulation of autophagy / liver development / platelet alpha granule lumen / epithelial cell proliferation / Negative regulation of MET activity / growth factor activity / cell morphogenesis / negative regulation of inflammatory response / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / Platelet degranulation / PIP3 activates AKT signaling / positive regulation of phosphatidylinositol 3-kinase signaling / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / positive regulation of MAPK cascade / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor binding / protein-containing complex binding / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / identical protein binding
Similarity search - Function
Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Hepatocyte Growth Factor / Hepatocyte Growth Factor / divergent subfamily of APPLE domains / Plasminogen Kringle 4 / Plasminogen Kringle 4 / PAN/Apple domain profile. / PAN domain / PAN/Apple domain ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Hepatocyte Growth Factor / Hepatocyte Growth Factor / divergent subfamily of APPLE domains / Plasminogen Kringle 4 / Plasminogen Kringle 4 / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 3-Layer(bba) Sandwich / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsTolbert, W.D. / Daugherty, J. / Gao, C.-F. / Xe, Q. / Miranti, C. / Gherardi, E. / Vande Woude, G. / Xu, H.E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist
Authors: Tolbert, W.D. / Daugherty, J. / Gao, C. / Xie, Q. / Miranti, C. / Gherardi, E. / Vande Woude, G. / Xu, H.E.
History
DepositionJul 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hepatocyte growth factor
B: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7036
Polymers42,3182
Non-polymers3844
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.401, 51.805, 73.167
Angle α, β, γ (deg.)90.00, 107.87, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the dimer in the asymmetric unit.

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Components

#1: Protein Hepatocyte growth factor /


Mass: 21159.236 Da / Num. of mol.: 2 / Fragment: residues 28-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE) / References: UniProt: P14210
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM ammonium sulfate, 26-29% PEG 4000 (w/w), 100 mM Tris-HCl pH 8.0, 0.5 mM beta-octyl glucoside, and 5% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.99998 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 20, 2004 / Details: monochromator Si 1 1 1
RadiationMonochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.8→22.3 Å / Num. all: 28061 / Num. obs: 28061 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 12.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1004 / Rsym value: 0.37 / % possible all: 31.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NK1

1nk1


Resolution: 1.81→22.29 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 256166.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Refined to a maximum likelihood target using amplitudes.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2647 9.9 %RANDOM
Rwork0.201 ---
all0.21 26701 --
obs0.201 26701 82.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.8867 Å2 / ksol: 0.446293 e/Å3
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20 Å22.41 Å2
2---1.52 Å20 Å2
3----1.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.81→22.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 20 330 3244
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 1.81→1.91 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 146 9.3 %
Rwork0.318 1429 -
obs-1575 28.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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