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- PDB-6gcu: MET receptor in complex with InlB internalin domain and DARPin A3A -

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Basic information

Entry
Database: PDB / ID: 6gcu
TitleMET receptor in complex with InlB internalin domain and DARPin A3A
Components
  • DARPin A3A
  • Hepatocyte growth factor receptor
  • Internalin B
KeywordsSIGNALING PROTEIN / receptor tyrosine kinase / bacterial invasion protein / artificial binding protein
Function / homology
Function and homology information


entry of bacterium into host cell / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / 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 / endothelial cell morphogenesis / semaphorin receptor activity ...entry of bacterium into host cell / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / 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 / endothelial cell morphogenesis / semaphorin receptor activity / 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 / positive regulation of endothelial cell chemotaxis / negative regulation of stress fiber assembly / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of Rho protein signal transduction / negative regulation of thrombin-activated receptor signaling pathway / semaphorin-plexin signaling pathway / establishment of skin barrier / MET activates RAS signaling / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / negative regulation of autophagy / cell surface receptor protein tyrosine kinase signaling pathway / peptidoglycan-based cell wall / basal plasma membrane / molecular function activator activity / InlB-mediated entry of Listeria monocytogenes into host cell / excitatory postsynaptic potential / liver development / Negative regulation of MET activity / receptor protein-tyrosine kinase / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / heparin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein phosphatase binding / cell surface receptor signaling pathway / receptor complex / postsynapse / lipid binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / metal ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal ...GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / : / Copper resistance protein CopC/internalin, immunoglobulin-like / Tyrosine-protein kinase, HGF/MSP receptor / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / 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 / IPT domain / Leucine-rich repeat, SDS22-like subfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin E-set / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / WD40/YVTN repeat-like-containing domain superfamily / 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
Similarity search - Domain/homology
Hepatocyte growth factor receptor / Internalin B / Internalin B
Similarity search - Component
Biological speciesHomo sapiens (human)
Listeria monocytogenes serovar 1/2a (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.001 Å
AuthorsMeyer, T. / Andres, F. / Iamele, L. / Gherardi, E. / Pluckthun, A. / Niemann, H.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNI 694/6-1 Germany
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Inhibition of the MET Kinase Activity and Cell Growth in MET-Addicted Cancer Cells by Bi-Paratopic Linking.
Authors: Andres, F. / Iamele, L. / Meyer, T. / Stuber, J.C. / Kast, F. / Gherardi, E. / Niemann, H.H. / Pluckthun, A.
History
DepositionApr 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 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 receptor
B: Internalin B
C: DARPin A3A
D: Hepatocyte growth factor receptor
E: Internalin B
F: DARPin A3A


Theoretical massNumber of molelcules
Total (without water)265,4136
Polymers265,4136
Non-polymers00
Water00
1
A: Hepatocyte growth factor receptor
B: Internalin B
C: DARPin A3A


Theoretical massNumber of molelcules
Total (without water)132,7073
Polymers132,7073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Hepatocyte growth factor receptor
E: Internalin B
F: DARPin A3A


Theoretical massNumber of molelcules
Total (without water)132,7073
Polymers132,7073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.874, 144.874, 128.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Hepatocyte growth factor receptor / 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: 81949.047 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): CHO lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P08581, receptor protein-tyrosine kinase
#2: Protein Internalin B


Mass: 32243.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: inlB, lmo0434 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25147, UniProt: P0DQD3*PLUS
#3: Protein DARPin A3A


Mass: 18513.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
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: 2.94 Å3/Da / Density % sol: 58.2 % / Description: hexagonal, pointy-ended rods
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium salt pH 7.5, 12% w/v PEG4000, protein complex concentration 5 mg/mL, equimolar ratio of macromolecules, drop size 0.2 uL, protein:reservoir ratio 1:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 6→48.15 Å / Num. obs: 7600 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 424 Å2 / CC1/2: 0.982 / R split: 0.136 / Rmerge(I) obs: 0.275 / Rpim(I) all: 0.107 / Rrim(I) all: 0.296 / Net I/σ(I): 5.2
Reflection shellResolution: 6→6.7 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.701 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2174 / CC1/2: 0.552 / Rpim(I) all: 0.646 / Rrim(I) all: 1.813 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_3071: ???)refinement
XDS20170923data reduction
Aimless0.5.32data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UZY

2uzy


Resolution: 6.001→48.149 Å / SU ML: 0.95 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.62
Details: Rigid body and grouped B-factor refinement of the separate domains (SEMA, PSI, IPT1, IPT2, InlB321, DARPin A3A)
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 339 4.49 %RANDOM
Rwork0.2625 ---
obs0.2629 7545 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 317.094 Å2
Refinement stepCycle: LAST / Resolution: 6.001→48.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17450 0 0 0 17450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01117826
X-RAY DIFFRACTIONf_angle_d1.76824196
X-RAY DIFFRACTIONf_dihedral_angle_d20.2736582
X-RAY DIFFRACTIONf_chiral_restr0.0962776
X-RAY DIFFRACTIONf_plane_restr0.0043130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.0009-7.55580.34191880.32573588X-RAY DIFFRACTION100
7.5558-48.15090.24021510.24093618X-RAY DIFFRACTION100

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