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- PDB-4k3j: Crystal structure of Onartuzumab Fab in complex with MET and HGF-beta -

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Basic information

Entry
Database: PDB / ID: 4k3j
TitleCrystal structure of Onartuzumab Fab in complex with MET and HGF-beta
Components
  • (Hepatocyte growth ...) x 2
  • (Onartuzumab Fab ...) x 2
KeywordsTransferase/Immune System/Growth Factor / antibody / glycosylation / Transferase-Immune System-Growth Factor complex
Function / homology
Function and homology information


regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / 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 ...regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / 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 / endothelial cell morphogenesis / hepatocyte growth factor receptor signaling pathway / semaphorin receptor activity / MET receptor recycling / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / myoblast proliferation / MET activates PI3K/AKT signaling / negative regulation of stress fiber assembly / positive regulation of endothelial cell chemotaxis / negative regulation of Rho protein signal transduction / MET activates PTK2 signaling / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / branching morphogenesis of an epithelial tube / positive chemotaxis / chemoattractant activity / negative regulation of thrombin-activated receptor signaling pathway / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / negative regulation of interleukin-6 production / semaphorin-plexin signaling pathway / positive regulation of interleukin-10 production / epithelial to mesenchymal transition / establishment of skin barrier / MET activates RAS signaling / positive regulation of osteoblast differentiation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / phagocytosis / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / Interleukin-7 signaling / negative regulation of autophagy / basal plasma membrane / cell chemotaxis / InlB-mediated entry of Listeria monocytogenes into host cell / excitatory postsynaptic potential / liver development / platelet alpha granule lumen / epithelial cell proliferation / molecular function activator activity / growth factor activity / cell morphogenesis / Negative regulation of MET activity / receptor protein-tyrosine kinase / neuron differentiation / negative regulation of inflammatory response / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / Platelet degranulation / PIP3 activates AKT signaling / mitotic cell cycle / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / postsynapse / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell surface receptor signaling pathway / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor binding / negative regulation of apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / divergent subfamily of APPLE domains / : / Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / divergent subfamily of APPLE domains / : / Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / IPT/TIG domain / ig-like, plexins, transcription factors / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Immunoglobulin E-set / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Thrombin, subunit H / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Peptidase S1, PA clan / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor receptor / Hepatocyte growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMa, X. / Starovasnik, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Monovalent antibody design and mechanism of action of onartuzumab, a MET antagonist with anti-tumor activity as a therapeutic agent.
Authors: Merchant, M. / Ma, X. / Maun, H.R. / Zheng, Z. / Peng, J. / Romero, M. / Huang, A. / Yang, N.Y. / Nishimura, M. / Greve, J. / Santell, L. / Zhang, Y.W. / Su, Y. / Kaufman, D.W. / Billeci, K. ...Authors: Merchant, M. / Ma, X. / Maun, H.R. / Zheng, Z. / Peng, J. / Romero, M. / Huang, A. / Yang, N.Y. / Nishimura, M. / Greve, J. / Santell, L. / Zhang, Y.W. / Su, Y. / Kaufman, D.W. / Billeci, K.L. / Mai, E. / Moffat, B. / Lim, A. / Duenas, E.T. / Phillips, H.S. / Xiang, H. / Young, J.C. / Vande Woude, G.F. / Dennis, M.S. / Reilly, D.E. / Schwall, R.H. / Starovasnik, M.A. / Lazarus, R.A. / Yansura, D.G.
History
DepositionApr 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Source and taxonomy
Revision 1.2Aug 20, 2014Group: Source and taxonomy
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hepatocyte growth factor
B: Hepatocyte growth factor beta chain
H: Onartuzumab Fab heavy chain
L: Onartuzumab Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,3825
Polymers135,1614
Non-polymers2211
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.191, 192.228, 65.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Hepatocyte growth ... , 2 types, 2 molecules AB

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


Mass: 26038.086 Da / Num. of mol.: 1 / Fragment: unp residues 495-721 / Mutation: C604S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14210
#2: Protein Hepatocyte growth factor beta chain / HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / ...HGF receptor / HGF/SF receptor / Proto-oncogene c-Met / Scatter factor receptor / SF receptor / Tyrosine-protein kinase Met


Mass: 60758.867 Da / Num. of mol.: 1 / Fragment: Sema and PSI domain, UNP residues 39-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P08581, receptor protein-tyrosine kinase

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Antibody , 2 types, 2 molecules HL

#3: Antibody Onartuzumab Fab heavy chain


Mass: 24000.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli)
#4: Antibody Onartuzumab Fab light chain


Mass: 24363.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli)

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Sugars / Non-polymers , 2 types, 184 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M sodium cacodylate pH 6.2, 20% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2011
RadiationMonochromator: Si 111 / Protocol: 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: 40382 / % possible obs: 98.9 % / Redundancy: 4 % / Rsym value: 0.074 / Net I/σ(I): 15.56
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.88 / Num. unique all: 3938 / Rsym value: 0.513 / % possible all: 98

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHY

1shy


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / SU B: 29.924 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.704 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25287 2027 5 %RANDOM
Rwork0.21083 ---
obs0.21297 38286 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.103 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å20 Å2
2---1.04 Å2-0 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9084 0 14 183 9281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229343
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.051.94912708
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95751157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18924.099405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.059151517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2991543
X-RAY DIFFRACTIONr_chiral_restr0.0690.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217081
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4491.55795
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85829404
X-RAY DIFFRACTIONr_scbond_it0.98233548
X-RAY DIFFRACTIONr_scangle_it1.7354.53304
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 156 -
Rwork0.324 2739 -
obs--97.51 %
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)
13.3001-1.51941.07633.9964-0.38643.0652-0.114-0.10380.35720.3418-0.04-0.5482-0.21030.30090.1540.0842-0.0188-0.05520.04920.00410.08514.981482.471910.1408
28.279-5.31195.790710.37343.004610.56920.5461-0.8315-1.61680.6523-1.17272.87291.1968-2.42490.62650.5929-0.10160.29451.0656-0.00390.9751-7.212273.322315.6565
34.3856-3.0075-0.0855.9175-0.50183.9426-0.2614-0.55050.17580.80950.23840.033-0.0685-0.1070.0230.22680.00090.03290.0954-0.01690.03575.205777.9915.903
44.47860.03891.46523.13550.51773.2651-0.12710.2620.7261-0.30770.12740.4358-0.45-0.1391-0.00030.1524-0.0427-0.05730.12550.12690.2325-11.474475.1304-15.4946
51.48270.31880.12942.843-0.41311.82660.00730.2113-0.2474-0.48320.0487-0.24360.27470.2416-0.0560.2086-0.0271-0.01960.15190.00330.08492.416553.9394-18.5801
63.38451.8694-0.52721.52160.04510.3162-0.0481-0.09840.22330.1201-0.13840.45620.0825-0.04940.18650.4114-0.1708-0.12460.4140.13820.5215-27.589645.7405-13.1449
70.5383-1.0060.81583.0625-1.91251.76140.22760.1774-0.0158-0.2288-0.3869-0.18390.17840.47090.15920.2697-0.01960.00370.34160.11540.254214.131416.15257.2439
81.1596-0.90340.87131.5618-1.13071.5934-0.0223-0.0798-0.05120.3284-0.0193-0.1078-0.19080.18120.04150.2632-0.0614-0.06710.26920.0950.24128.035720.0823.7848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A495 - 636
2X-RAY DIFFRACTION2A637 - 661
3X-RAY DIFFRACTION3A662 - 721
4X-RAY DIFFRACTION4B39 - 212
5X-RAY DIFFRACTION5B213 - 454
6X-RAY DIFFRACTION6B455 - 564
7X-RAY DIFFRACTION7H1 - 215
8X-RAY DIFFRACTION8L1 - 211

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