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- PDB-6i04: Crystal structure of Sema domain of the Met receptor in complex w... -

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Basic information

Entry
Database: PDB / ID: 6i04
TitleCrystal structure of Sema domain of the Met receptor in complex with FAB
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Hepatocyte growth factor receptorC-Met
KeywordsIMMUNE SYSTEM / MET / Sema domain
Function / homology
Function and homology information


hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / semaphorin receptor activity / positive regulation of endothelial cell chemotaxis ...hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / semaphorin receptor activity / positive regulation of endothelial cell chemotaxis / MET receptor recycling / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / MET activates PI3K/AKT signaling / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of thrombin-activated receptor signaling pathway / semaphorin-plexin signaling pathway / establishment of skin barrier / MET activates RAS signaling / phagocytosis / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / basal plasma membrane / negative regulation of autophagy / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / molecular function activator activity / Negative regulation of MET activity / receptor protein-tyrosine kinase / neuron differentiation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / cell surface receptor signaling pathway / receptor complex / phosphorylation / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain ...Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin E-set / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCasaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. ...Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. / Logan, D.T. / Welin, M. / Chattopadhyay, S. / Harms, B.D. / Nielsen, U.B. / Schoeberl, B. / Lugovskoy, A.A. / MacBeath, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: MM-131, a bispecific anti-Met/EpCAM mAb, inhibits HGF-dependent and HGF-independent Met signaling through concurrent binding to EpCAM.
Authors: Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. ...Authors: Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. / Logan, D.T. / Welin, M. / Chattopadhyay, S. / Harms, B.D. / Nielsen, U.B. / Schoeberl, B. / Lugovskoy, A.A. / MacBeath, G.
History
DepositionOct 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 receptor
H: Fab heavy chain
L: Fab light chain
B: Hepatocyte growth factor receptor
C: Fab heavy chain
D: Fab light chain


Theoretical massNumber of molelcules
Total (without water)219,9966
Polymers219,9966
Non-polymers00
Water0
1
A: Hepatocyte growth factor receptor
H: Fab heavy chain
L: Fab light chain


Theoretical massNumber of molelcules
Total (without water)109,9983
Polymers109,9983
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-40 kcal/mol
Surface area36540 Å2
MethodPISA
2
B: Hepatocyte growth factor receptor
C: Fab heavy chain
D: Fab light chain


Theoretical massNumber of molelcules
Total (without water)109,9983
Polymers109,9983
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-40 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.932, 85.497, 101.300
Angle α, β, γ (deg.)77.49, 88.58, 68.76
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12H
22C
13L
23D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRGLYGLYAA41 - 51717 - 493
21TYRTYRGLYGLYBD41 - 51717 - 493
12GLNGLNLYSLYSHB1 - 2191 - 219
22GLNGLNLYSLYSCE1 - 2191 - 219
13ASPASPGLYGLYLC1 - 2121 - 212
23ASPASPGLYGLYDF1 - 2121 - 212

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Hepatocyte growth factor receptor / C-Met / 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: 62404.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Cell line (production host): EXPI293F cells / Production host: Homo sapiens (human)
References: UniProt: P08581, receptor protein-tyrosine kinase
#2: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 24478.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293F cells / Production host: Homo sapiens (human)
#3: Antibody Fab light chain / Fragment antigen-binding


Mass: 23114.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293F cells / Production host: Homo sapiens (human)

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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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18% w/v PEG 3350, 0.1 M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→29.57 Å / Num. obs: 39528 / % possible obs: 96.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 71 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.169 / Net I/σ(I): 5.2
Reflection shellResolution: 3.1→3.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.033 / Mean I/σ(I) obs: 1 / Num. unique obs: 3994 / CC1/2: 0.446 / % possible all: 86.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PY7, 4O3T

4py7

4o3t


Resolution: 3.1→29.56 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 29.744 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.497 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26105 1983 5 %RANDOM
Rwork0.20167 ---
obs0.20455 37543 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.843 Å2
Baniso -1Baniso -2Baniso -3
1-5.63 Å2-1.3 Å2-1.04 Å2
2--0.32 Å20.44 Å2
3----5.97 Å2
Refinement stepCycle: 1 / Resolution: 3.1→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13366 0 0 0 13366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01313701
X-RAY DIFFRACTIONr_bond_other_d0.0020.01712337
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.64118642
X-RAY DIFFRACTIONr_angle_other_deg1.21.56728794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72851704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76923.365627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.51152217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.041550
X-RAY DIFFRACTIONr_chiral_restr0.0530.21841
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022763
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_it5.0798.7516873
X-RAY DIFFRACTIONr_mcbond_other5.0788.7526871
X-RAY DIFFRACTIONr_mcangle_it8.04513.1228558
X-RAY DIFFRACTIONr_mcangle_other8.04513.1228558
X-RAY DIFFRACTIONr_scbond_it5.2919.266828
X-RAY DIFFRACTIONr_scbond_other5.2919.266829
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.51813.68610085
X-RAY DIFFRACTIONr_long_range_B_refined13.47252262
X-RAY DIFFRACTIONr_long_range_B_other13.47352258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A130620.06
12B130620.06
21H63200.03
22C63200.03
31L62840.05
32D62840.05
LS refinement shellResolution: 3.104→3.184 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 135 -
Rwork0.36 2277 -
obs--80.27 %

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