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- PDB-6lz9: t8E4 antibody Fab complexed with the active form of HGF -

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Basic information

Entry
Database: PDB / ID: 6lz9
Titlet8E4 antibody Fab complexed with the active form of HGF
Components
  • (Hepatocyte growth factor) x 2
  • Heavy chain of t8E4 Fab fragment
  • Light chain of t8E4 Fab fragment
KeywordsIMMUNE SYSTEM / antibody / HGF / hepatocyte growth factor / active form
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 / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKitago, Y. / Umitsu, M. / Takagi, J.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)19am0101075 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP17H01420 Japan
Citation
Journal: To Be Published
Title: t8E4 antibody Fab complexed with the active form of HGF
Authors: Umitsu, M. / Kitago, Y. / Takagi, J.
#1: Journal: Sci Rep / Year: 2016
Title: Probing conformational and functional states of human hepatocyte growth factor by a panel of monoclonal antibodies.
Authors: Umitsu, M. / Sakai, K. / Ogasawara, S. / Kaneko, M.K. / Asaki, R. / Tamura-Kawakami, K. / Kato, Y. / Matsumoto, K. / Takagi, J.
History
DepositionFeb 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
H: Heavy chain of t8E4 Fab fragment
L: Light chain of t8E4 Fab fragment


Theoretical massNumber of molelcules
Total (without water)87,3104
Polymers87,3104
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.180, 176.180, 122.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein Hepatocyte growth factor / / Hepatopoietin-A / Scatter factor / SF


Mass: 12280.603 Da / Num. of mol.: 1 / Fragment: K4 domain / Mutation: N402Q, T476G, K491I, Q492E, L493G
Source method: isolated from a genetically manipulated source
Details: This molecule was produced as one polypeptide with chain B, and this chain if N-terminal portion. After the artificial enzymatic cleavage with Factor Xa, they are connected with each other by a disulfide bond.
Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P14210
#2: Protein Hepatocyte growth factor / / Hepatopoietin-A / Scatter factor / SF


Mass: 27107.373 Da / Num. of mol.: 1 / Fragment: SP domain / Mutation: C561S, N566Q, N653Q
Source method: isolated from a genetically manipulated source
Details: This molecule was produced as one polypeptide with chain A, and this chain if C-terminal portion. After the artificial enzymatic cleavage with Factor Xa, they are connected with each other by a disulfide bond.
Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P14210
#3: Antibody Heavy chain of t8E4 Fab fragment


Mass: 24075.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PCA residue at the N-terminus is the self-cyclized Gln residue.
Source: (gene. exp.) Mus musculus (house mouse) / Description: B cells fused with myeloma cells / Cell (production host): hybridoma / Production host: hybrid (others)
#4: Antibody Light chain of t8E4 Fab fragment


Mass: 23847.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: B cells fused with myeloma cells / Cell (production host): hybridoma / Production host: hybrid (others)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 % (w/v) PEG 10000, 0.1M Magnesium acetate, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 28218 / % possible obs: 99.7 % / Redundancy: 9.9 % / Biso Wilson estimate: 72.92 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.8
Reflection shellResolution: 2.8→2.97 Å / Num. unique obs: 4412 / CC1/2: 0.673

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SHY, 1OPG

1shy

1opg


Resolution: 2.8→47.87 Å / SU ML: 0.5316 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2975 1362 4.85 %
Rwork0.2482 26744 -
obs0.2506 28106 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.66 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5023 0 0 5 5028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00685145
X-RAY DIFFRACTIONf_angle_d0.97067014
X-RAY DIFFRACTIONf_chiral_restr0.0513796
X-RAY DIFFRACTIONf_plane_restr0.0062891
X-RAY DIFFRACTIONf_dihedral_angle_d19.98631810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.49731350.4432606X-RAY DIFFRACTION99.42
2.9-3.020.41011300.36392602X-RAY DIFFRACTION99.38
3.02-3.150.35841280.31512641X-RAY DIFFRACTION99.32
3.15-3.320.32491320.27822633X-RAY DIFFRACTION99.6
3.32-3.530.34091280.2662648X-RAY DIFFRACTION99.75
3.53-3.80.32251450.26622634X-RAY DIFFRACTION100
3.8-4.180.27771510.2142655X-RAY DIFFRACTION99.72
4.18-4.790.23291320.18612706X-RAY DIFFRACTION99.96
4.79-6.030.25341440.21572727X-RAY DIFFRACTION99.97
6.03-47.870.29751370.25632892X-RAY DIFFRACTION99.41
Refinement TLS params.Method: refined / Origin x: 29.1260065328 Å / Origin y: 63.1646002203 Å / Origin z: 32.4677032777 Å
111213212223313233
T0.462367137996 Å20.243553671491 Å2-0.022692393411 Å2-0.744598728384 Å2-0.0269263440619 Å2--0.600453811156 Å2
L0.092640675664 °20.167332824822 °20.233806870869 °2-0.655833837357 °20.236605922589 °2--0.878443744717 °2
S-0.0292810727711 Å °-0.0623325263748 Å °0.00611191132443 Å °0.12305462482 Å °0.0631613910953 Å °0.0752109106947 Å °0.234326613604 Å °0.0103015896219 Å °-0.0311226856377 Å °
Refinement TLS groupSelection details: all

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