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- PDB-2ks1: Heterodimeric association of Transmembrane domains of ErbB1 and E... -

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Basic information

Entry
Database: PDB / ID: 2ks1
TitleHeterodimeric association of Transmembrane domains of ErbB1 and ErbB2 receptors Enabling Kinase Activation
Components
  • Epidermal growth factor receptor
  • Receptor tyrosine-protein kinase erbB-2
KeywordsTRANSFERASE / ErbB1 / ErbB2 / transmembrane / heterodimer / complex / tyrosine kinase receptor / bicelles
Function / homology
Function and homology information


negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / regulation of microtubule-based process / ErbB-3 class receptor binding / Sema4D induced cell migration and growth-cone collapse ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / regulation of microtubule-based process / ErbB-3 class receptor binding / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / neurotransmitter receptor localization to postsynaptic specialization membrane / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / positive regulation of Rho protein signal transduction / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / regulation of nitric-oxide synthase activity / ERBB2 Activates PTK6 Signaling / morphogenesis of an epithelial fold / neuromuscular junction development / intracellular vesicle / Signaling by EGFR / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / enzyme-linked receptor protein signaling pathway / response to cobalamin / negative regulation of epidermal growth factor receptor signaling pathway / transmembrane receptor protein tyrosine kinase activator activity / ERBB2-ERBB3 signaling pathway / protein tyrosine kinase activator activity / positive regulation of transcription by RNA polymerase I / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signaling by ERBB4 / eyelid development in camera-type eye / oligodendrocyte differentiation / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / regulation of JNK cascade / semaphorin-plexin signaling pathway / activation of phospholipase C activity / positive regulation of cyclin-dependent protein serine/threonine kinase activity / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / negative regulation of mitotic cell cycle / hair follicle development / positive regulation of cell adhesion / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / positive regulation of bone resorption / GAB1 signalosome / regulation of angiogenesis / positive regulation of nitric oxide mediated signal transduction / coreceptor activity / Schwann cell development / salivary gland morphogenesis / regulation of peptidyl-tyrosine phosphorylation / peptidyl-tyrosine autophosphorylation / positive regulation of glial cell proliferation / positive regulation of phosphorylation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / cellular response to cadmium ion / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / positive regulation of DNA repair / EGFR Transactivation by Gastrin / myelination / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling
Similarity search - Function
Cytochrome c1, transmembrane anchor, C-terminal / Immunoglobulin FC, subunit C / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily ...Cytochrome c1, transmembrane anchor, C-terminal / Immunoglobulin FC, subunit C / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Epidermal growth factor receptor / Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsMineev, K.S. / Bocharov, E.V. / Pustovalova, Y.E. / Bocharova, O.V. / Chupin, V.V. / Arseniev, A.S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Spatial Structure of the Transmembrane Domain Heterodimer of ErbB1 and ErbB2 Receptor Tyrosine Kinases
Authors: Mineev, K.S. / Bocharov, E.V. / Pustovalova, Y.E. / Bocharova, O.V. / Chupin, V.V. / Arseniev, A.S.
History
DepositionDec 24, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor tyrosine-protein kinase erbB-2
B: Epidermal growth factor receptor


Theoretical massNumber of molelcules
Total (without water)9,4692
Polymers9,4692
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Receptor tyrosine-protein kinase erbB-2 / p185erbB2 / C-erbB-2 / NEU proto-oncogene / Tyrosine kinase-type cell surface receptor HER2 / MLN 19


Mass: 4734.805 Da / Num. of mol.: 1 / Fragment: ErbB2TM domain, UNP residues 641-684
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2, HER2, NEU, NGL / Production host: Escherichia coli (E. coli)
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Protein/peptide Epidermal growth factor receptor / / Receptor tyrosine-protein kinase ErbB-1


Mass: 4733.849 Da / Num. of mol.: 1 / Fragment: ErbB1TM domain, UNP residues 634-677
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00533, receptor protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the heterodimeric complex fromed by transmembrane segments of ErbB1 and ErbB2 receptors inlipidic bicelles
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1333D HNCA
1433D HN(CO)CA
1533D 1H-15N NOESY
1633D 1H-15N TOCSY
1723D (H)CCH-TOCSY
1823D 1H-13C NOESY
1923d-13Cfilt NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] ErbB1TM-1, 1 mM [U-100% 15N] ErbB2TM-2, 12 mM DMPC-3, 48 mM DHPC-4, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] ErbB1TM-5, 1 mM ErbB2TM-6, 12 mM [U-2H] DMPC-7, 48 mM [U-2H] DHPC-8, 100% D2O100% D2O
31 mM ErbB1TM-9, 1 mM [U-100% 13C; U-100% 15N] ErbB2TM-10, 12 mM [U-2H] DMPC-11, 48 mM [U-2H] DHPC-12, 95% H2O/5% D2O95% H2O/5% D2O
41 mM [U-100% 13C; U-100% 15N] ErbB1TM-13, 1 mM ErbB2TM-14, 12 mM [U-2H] DMPC-15, 48 mM [U-2H] DHPC-16, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMErbB1TM-1[U-100% 15N]1
1 mMErbB2TM-2[U-100% 15N]1
12 mMDMPC-31
48 mMDHPC-41
1 mMErbB1TM-5[U-100% 13C; U-100% 15N]2
1 mMErbB2TM-62
12 mMDMPC-7[U-2H]2
48 mMDHPC-8[U-2H]2
1 mMErbB1TM-93
1 mMErbB2TM-10[U-100% 13C; U-100% 15N]3
12 mMDMPC-11[U-2H]3
48 mMDHPC-12[U-2H]3
1 mMErbB1TM-13[U-100% 13C; U-100% 15N]4
1 mMErbB2TM-144
12 mMDMPC-15[U-2H]4
48 mMDHPC-16[U-2H]4
Sample conditionsIonic strength: 10 / pH: 4.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospinprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 722 / NOE intraresidue total count: 382 / NOE long range total count: 13 / NOE medium range total count: 123 / NOE sequential total count: 204
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 12 / Maximum upper distance constraint violation: 0.2 Å / Representative conformer: 1

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