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- PDB-3mkp: Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatt... -

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Basic information

Entry
Database: PDB / ID: 3mkp
TitleCrystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatter Factor fragment NK1 in complex with heparin
ComponentsHepatocyte growth factor
KeywordsHORMONE / growth factor / supramolecular assembly / HGF/SF / Met receptor / NK1
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 / cellular response to hepatocyte growth factor stimulus / positive regulation of DNA biosynthetic process / chemoattractant activity / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / 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 extrinsic apoptotic signaling pathway via death domain receptors / Interleukin-7 signaling / negative regulation of autophagy / cell chemotaxis / 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 / 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 / identical protein binding / membrane
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
Chem-SGN / Hepatocyte growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsGherardi, E. / Chirgadze, D.Y. / Blundell, T.L.
Citation
Journal: To be Published
Title: Engineering a fragment of Hepatocyte Growth Factor/Scatter Factor for tissue and organ regeneration
Authors: Gherardi, E. / Chirgadze, D.Y. / Bocci, M. / Brocchieri, C. / Bevan, D. / Kajstura, J. / Esposito, G. / Lietha, D. / Rota, M. / Leri, A. / Mallorqui-Fernandez, N. / Bandyopadhyay, A. / ...Authors: Gherardi, E. / Chirgadze, D.Y. / Bocci, M. / Brocchieri, C. / Bevan, D. / Kajstura, J. / Esposito, G. / Lietha, D. / Rota, M. / Leri, A. / Mallorqui-Fernandez, N. / Bandyopadhyay, A. / Youles, M. / Mulloy, B. / Rowe, A. / Alison, M. / Edwards, D. / Vannini, V. / Blundell, T. / Anversa, P.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Coupling growth-factor engineering with nanotechnology for therapeutic angiogenesis
Authors: Roy, R.S. / Soni, S. / Harfouche, R. / Vasudevan, P.R. / Holmes, O. / de Jonge, H. / Rowe, A. / Paraskar, A. / Hentschel, D.M. / Chirgadze, D. / Blundell, T.L. / Gherardi, E. / Mashelkar, R.A. / Sengupta, S.
History
DepositionApr 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Hepatocyte growth factor
D: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,89114
Polymers84,4644
Non-polymers3,42710
Water1,820101
1
A: Hepatocyte growth factor
B: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2407
Polymers42,2322
Non-polymers1,0085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-6 kcal/mol
Surface area17040 Å2
MethodPISA
2
C: Hepatocyte growth factor
D: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6517
Polymers42,2322
Non-polymers2,4195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-2 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.73, 129.73, 118.19
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 21116.074 Da / Num. of mol.: 4 / Fragment: UNP residues 28-210 / Mutation: K132E, R134E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPIC9K / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P14210

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1750.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,6,5/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{}}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-SGN / 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose / N,O6-DISULFO-GLUCOSAMINE / 6-O-sulfo-N-sulfo-alpha-D-glucosamine / 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucose / 2-deoxy-6-O-sulfo-2-(sulfoamino)-D-glucose / 2-deoxy-6-O-sulfo-2-(sulfoamino)-glucose


Type: D-saccharide, alpha linking / Mass: 339.298 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO11S2
IdentifierTypeProgram
DGlcpNS[6S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-sulfo-6-sulfo-a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpNSO36SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 109 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.243M Ammonium Sulfate, 22.295% PEG 3350, 0.1M Na-Hepes pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 25301 / Num. obs: 25225 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 7.9 % / Biso Wilson estimate: 61.7 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.498 / Num. unique all: 1661 / Rsym value: 0.498 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BHT

1bht


Resolution: 2.81→49.69 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.862 / SU B: 26.614 / SU ML: 0.267 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.489 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1287 5.1 %RANDOM
Rwork0.199 ---
all0.202 23960 --
obs0.202 23907 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.405 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.81→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5461 0 204 101 5766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225824
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9857885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4495684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10223.861259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.45115990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2111534
X-RAY DIFFRACTIONr_chiral_restr0.0890.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024292
X-RAY DIFFRACTIONr_nbd_refined0.2140.22469
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23896
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.210
X-RAY DIFFRACTIONr_mcbond_it2.1253497
X-RAY DIFFRACTIONr_mcangle_it3.31165549
X-RAY DIFFRACTIONr_scbond_it2.69252599
X-RAY DIFFRACTIONr_scangle_it4.147.52336
LS refinement shellResolution: 2.807→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 91 -
Rwork0.262 1758 -
obs-1849 99.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.40320.6772.72565.3743-1.14872.7009-0.153-0.2386-0.3552-0.00640.3845-0.03280.0456-0.4664-0.2315-0.0860-0.01080.0740.0358-0.14440.20419.01222.619
27.08550.85730.93590.71520.72971.63030.10050.08660.0931-0.0839-0.11010.038-0.0977-0.03160.0096-0.0312-0.0062-0.0165-0.0405-0.0384-0.052718.09835.57916.446
34.4332-0.5326-0.28362.37781.22824.9292-0.09810.35150.0983-0.17650.0932-0.08660.12110.50040.0049-0.0485-0.007-0.02440.0855-0.0067-0.14644.81432.631-4.686
44.02070.84850.95910.61530.33331.4173-0.0041-0.6210.16290.0112-0.06360.0925-0.0621-0.24670.0677-0.05550.0492-0.02020.1028-0.0651-0.0584-16.13933.2339.803
53.49610.53591.44274.356-0.29680.7466-0.0118-0.03470.0002-0.04-0.0705-0.05590.09890.0070.0822-0.0588-0.0014-0.00710.05580.0214-0.1294-0.30722.352-34.49
68.88032.1258-0.6812.64860.32641.65150.2066-0.01690.4303-0.035-0.3564-0.3626-0.28620.22040.1497-0.1458-0.1014-0.04030.04790.13540.085312.5142.205-43.324
76.6547-1.1934-0.07864.61493.115910.67180.10110.26760.1772-0.8199-0.36080.06710.16340.5210.25970.05180.12920.04870.01570.1164-0.0621-1.56336.429-64.24
82.06650.39230.21862.159-0.38351.58460.0941-0.18220.0206-0.0553-0.0929-0.1014-0.06210.0078-0.0012-0.04190.00980.005-0.0326-0.05070.0002-20.04331.347-47.072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 126
2X-RAY DIFFRACTION2A127 - 208
3X-RAY DIFFRACTION3B36 - 126
4X-RAY DIFFRACTION4B127 - 208
5X-RAY DIFFRACTION5C36 - 126
6X-RAY DIFFRACTION6C127 - 208
7X-RAY DIFFRACTION7D40 - 126
8X-RAY DIFFRACTION8D127 - 208

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