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- PDB-3sp8: Crystal structure of NK2 in complex with fractionated Heparin DP10 -

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Basic information

Entry
Database: PDB / ID: 3sp8
TitleCrystal structure of NK2 in complex with fractionated Heparin DP10
ComponentsHepatocyte growth factor alpha chain
KeywordsHORMONE / kringle domain / MET Tyrosine Kinase
Function / homology
Function and homology information


regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling ...regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling / MET activates PTPN11 / MET activates RAP1 and RAC1 / myoblast proliferation / MET activates PI3K/AKT signaling / MET activates PTK2 signaling / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / MET activates RAS signaling / negative regulation of peptidyl-serine phosphorylation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Interleukin-7 signaling / cell chemotaxis / negative regulation of autophagy / platelet alpha granule lumen / liver development / epithelial cell proliferation / growth factor activity / cell morphogenesis / Negative regulation of MET activity / negative regulation of inflammatory response / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / Platelet degranulation / PIP3 activates AKT 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 phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor 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 / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / 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: 1.86 Å
AuthorsRecacha, R. / Mulloy, B. / Gherardi, E.
Citation
Journal: TO BE PUBLISHED
Title: Crystal structure of NK2 in complex with fractionated Heparin DP10
Authors: Recacha, R. / Mulloy, B. / Gherardi, E.
#1: Journal: Embo J. / Year: 2001
Title: Crystal structures of NK1 heparin complexes reveal the basis for NK1 activity and enable engineering of potent agonists of the MET receptor
Authors: Lietha, D. / Chirgadze, D.Y. / L Blundell, T. / Gherardi, E. / Mulloy, B.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for agonism and antagonism of hepatocyte growth factor
Authors: Tolbert, W.D. / Daugherty-Holtrop, J. / Vande Woude, G. / Xu, H.E. / Gherardi, E.
#3: Journal: J.Biol.Chem. / Year: 2008
Title: Heparin-induced cis- and trans-Dimerization Modes of the Thrombospondin-1 N-terminal Domain
Authors: Tan, K. / Duquette, M. / Liu, J.H. / Shanmugasundaram, K. / Joachimiak, A. / Gallagher, J.T. / Rigby, A.C. / Wang, J.H. / Lawler, J.
History
DepositionJul 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,15321
Polymers61,8202
Non-polymers2,33219
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hepatocyte growth factor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,35013
Polymers30,9101
Non-polymers1,44012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Hepatocyte growth factor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8038
Polymers30,9101
Non-polymers8937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.980, 75.980, 199.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hepatocyte growth factor alpha chain / Hepatopoeitin-A / Scatter factor / SF


Mass: 30910.119 Da / Num. of mol.: 2 / Fragment: NK2 / Mutation: G146D, C214S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Production host: Pichia Pastoris (fungus) / References: UniProt: P14210

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Non-polymers , 5 types, 378 molecules

#2: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM MES pH=6.0, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 21K, temperature 294K

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Data collection

DiffractionMean temperature: 172 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.86→65.8 Å / Num. all: 107330 / Num. obs: 54379 / % possible obs: 99.76 % / Observed criterion σ(F): 1.38
Reflection shellHighest resolution: 1.86 Å / % possible all: 99.76

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NH4

3nh4


Resolution: 1.86→65.8 Å / SU ML: 0.57 / Cross valid method: Maximum Likelyhood / σ(F): 1.38 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 2763 5.08 %Random
Rwork0.1868 ---
obs0.1883 54379 99.76 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.503 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0152 Å20 Å20 Å2
2---1.0152 Å2-0 Å2
3---2.0303 Å2
Refinement stepCycle: LAST / Resolution: 1.86→65.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 138 359 4673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044630
X-RAY DIFFRACTIONf_angle_d0.8836270
X-RAY DIFFRACTIONf_dihedral_angle_d16.3791808
X-RAY DIFFRACTIONf_chiral_restr0.062608
X-RAY DIFFRACTIONf_plane_restr0.004805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.89210.36971630.3182570X-RAY DIFFRACTION100
1.8921-1.92650.30251490.28972552X-RAY DIFFRACTION100
1.9265-1.96360.29621430.25582560X-RAY DIFFRACTION100
1.9636-2.00370.30431540.25792581X-RAY DIFFRACTION100
2.0037-2.04720.28541440.22622559X-RAY DIFFRACTION100
2.0472-2.09490.29471260.21272602X-RAY DIFFRACTION100
2.0949-2.14730.25361290.20652570X-RAY DIFFRACTION100
2.1473-2.20530.20761210.1962586X-RAY DIFFRACTION100
2.2053-2.27020.24141430.19642569X-RAY DIFFRACTION100
2.2702-2.34350.23941330.20352592X-RAY DIFFRACTION100
2.3435-2.42720.25211360.19812577X-RAY DIFFRACTION100
2.4272-2.52440.22291330.19932613X-RAY DIFFRACTION100
2.5244-2.63930.24761340.19382578X-RAY DIFFRACTION100
2.6393-2.77850.23911290.19432576X-RAY DIFFRACTION100
2.7785-2.95260.1991270.18872616X-RAY DIFFRACTION100
2.9526-3.18050.20511640.18362562X-RAY DIFFRACTION100
3.1805-3.50060.19361460.18222567X-RAY DIFFRACTION100
3.5006-4.00710.19361330.16062600X-RAY DIFFRACTION100
4.0071-5.04820.17021210.14762612X-RAY DIFFRACTION100
5.0482-65.84170.21181350.19492574X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -29.1929 Å / Origin y: 26.8444 Å / Origin z: -16.1371 Å
111213212223313233
T0.3089 Å20.0272 Å20.004 Å2-0.2744 Å2-0.0178 Å2--0.2348 Å2
L0.5482 °2-0.3342 °20.2864 °2-0.9968 °2-0.5337 °2--0.4659 °2
S-0.1157 Å °-0.1456 Å °0.0438 Å °-0.1346 Å °0.0488 Å °-0.0685 Å °0.0462 Å °-0.1067 Å °0.0596 Å °
Refinement TLS groupSelection details: all

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