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- PDB-7ocm: K1K1H6, a potent recombinant minimal hepatocyte growth factor/sca... -

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Basic information

Entry
Database: PDB / ID: 7ocm
TitleK1K1H6, a potent recombinant minimal hepatocyte growth factor/scatter factor mimic
ComponentsHepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain
KeywordsDE NOVO PROTEIN / MET receptor agonist / HGF/SF kringle 1 dimer / HGF/SF-derived recombinant protein / MET-activator / regeneration of epithelial tissue and organs / engineered growth factor
Function / homology
Function and homology information


regulation of p38MAPK cascade / skeletal muscle cell proliferation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / 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 / hepatocyte growth factor receptor signaling pathway / MET receptor recycling ...regulation of p38MAPK cascade / skeletal muscle cell proliferation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / 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 / hepatocyte growth factor receptor signaling pathway / MET receptor recycling / MET activates PTPN11 / MET activates RAP1 and RAC1 / 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 / myoblast proliferation / 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 / platelet alpha granule lumen / epithelial cell proliferation / cell chemotaxis / growth factor activity / liver development / Negative regulation of MET activity / negative regulation of inflammatory response / cell morphogenesis / 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 phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / 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 / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / 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 / 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
Similarity search - Domain/homology
Hepatocyte growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
Authorsde Jonge, H. / de Nola, G. / Gherardi, E.
CitationJournal: Life Sci Alliance / Year: 2022
Title: Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent MET receptor agonist.
Authors: de Nola, G. / Leclercq, B. / Mougel, A. / Taront, S. / Simonneau, C. / Forneris, F. / Adriaenssens, E. / Drobecq, H. / Iamele, L. / Dubuquoy, L. / Melnyk, O. / Gherardi, E. / de Jonge, H. / Vicogne, J.
History
DepositionApr 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,5383
Polymers20,0621
Non-polymers4772
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: no macromolecular assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint13 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.839, 59.648, 46.289
Angle α, β, γ (deg.)90.000, 103.850, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Hepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain


Mass: 20061.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Production host: Escherichia coli (E. coli) / References: UniProt: P14210
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.16 % / Description: Thin hexagonal shaped
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM MOPS/HEPES pH 7.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 20% v/v glycerol, 10% w/v PEG4000
Temp details: Inside a fridge-like incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 29, 2014 / Details: Toroidal mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.26→44.94 Å / Num. obs: 45262 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.041 / Rrim(I) all: 0.081 / Net I/σ(I): 8.4 / Num. measured all: 167746
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.26-1.33.51.4241520044040.3920.891.6870.999.2
4.88-44.943.80.06331288200.9930.0360.07328.399.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XSCALEVERSION January 10, 2014 BUILT=20140115data scaling
PHASER2.8.3phasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BHT

1bht


Resolution: 1.7→35.89 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1945 961 5.18 %
Rwork0.1637 --
obs0.1653 18549 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.43 Å2 / Biso mean: 22.03 Å2 / Biso min: 7.92 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1382 0 30 122 1534
LS refinement shellResolution: 1.7→1.79 Å
RfactorNum. reflection% reflection
Rfree0.1902 146 -
Rwork0.1607 2493 -
obs--99.81 %

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