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- PDB-5ob4: NMR spatial structure of HER2 TM domain dimer in DPC micelles. -

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Basic information

Entry
Database: PDB / ID: 5ob4
TitleNMR spatial structure of HER2 TM domain dimer in DPC micelles.
ComponentsReceptor tyrosine-protein kinase erbB-2
KeywordsMEMBRANE PROTEIN / PROTEIN ERBB2 HER2 RECEPTOR TYROSINE KINASE MEMBRANE DOMAIN DIMER
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 / ErbB-3 class receptor binding / regulation of microtubule-based process / 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 / ErbB-3 class receptor binding / regulation of microtubule-based process / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / positive regulation of Rho protein signal transduction / ERBB2 Activates PTK6 Signaling / neuromuscular junction development / positive regulation of transcription by RNA polymerase I / 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 / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / regulation of angiogenesis / coreceptor activity / Schwann cell development / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / myelination / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of ERK1 and ERK2 cascade / SHC1 events in ERBB2 signaling / positive regulation of cell adhesion / Downregulation of ERBB2:ERBB3 signaling / Constitutive Signaling by Overexpressed ERBB2 / neurogenesis / positive regulation of epithelial cell proliferation / basal plasma membrane / positive regulation of translation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / Signaling by ERBB2 ECD mutants / neuromuscular junction / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / neuron differentiation / cellular response to growth factor stimulus / receptor tyrosine kinase binding / Downregulation of ERBB2 signaling / peptidyl-tyrosine phosphorylation / ruffle membrane / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / heart development / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of cell growth / basolateral plasma membrane / positive regulation of MAPK cascade / early endosome / receptor complex / cell surface receptor signaling pathway / endosome membrane / intracellular signal transduction / protein heterodimerization activity / positive regulation of protein phosphorylation / protein phosphorylation / apical plasma membrane / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
: / 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 ...: / 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 / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMineev, K.S. / Arseniev, A.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-14-00573 Russian Federation
CitationJournal: J. Biomol. NMR / Year: 2017
Title: NMR relaxation parameters of methyl groups as a tool to map the interfaces of helix-helix interactions in membrane proteins.
Authors: Lesovoy, D.M. / Mineev, K.S. / Bragin, P.E. / Bocharova, O.V. / Bocharov, E.V. / Arseniev, A.S.
History
DepositionJun 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Receptor tyrosine-protein kinase erbB-2


Theoretical massNumber of molelcules
Total (without water)9,4702
Polymers9,4702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Dimer was confirmed by the isotope-filtered NMR spectra and titration experiments
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area700 Å2
ΔGint-11 kcal/mol
Surface area8670 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Receptor tyrosine-protein kinase erbB-2 / Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / ...Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / Tyrosine kinase-type cell surface receptor HER2 / p185erbB2


Mass: 4734.805 Da / Num. of mol.: 2 / Fragment: UNP residues 31-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2, HER2, MLN19, NEU, NGL / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P04626, receptor protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HNCO
131isotropic13D (H)CCH-TOCSY
141isotropic13D 1H-13C NOESY aliphatic
151isotropic13D 1H-15N NOESY
161isotropic13D 13C-filtered NOESY

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Sample preparation

DetailsType: micelle
Contents: 2.5 mM [U-100% 13C; U-100% 15N] HER2TM, 2.5 mM HER2TM, 200 mM [U-99% 2H] DPC, 20 mM potassium phosphate, 0.01 % sodium azide, 90% H2O/10% D2O
Details: sample in DPC micelles / Label: s1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMHER2TM_label[U-100% 13C; U-100% 15N]1
2.5 mMHER2TMnatural abundance1
200 mMDPC[U-99% 2H]1
20 mMpotassium phosphatenatural abundance1
0.01 %sodium azidenatural abundance1
Sample conditionsIonic strength: 30 mM / Label: conditions_1 / pH: 6 / PH err: 0.1 / Pressure: AMBIENT Pa / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.8.4Keller and Wuthrichchemical shift assignment
TopSpinBruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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