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- PDB-1iij: SOLUTION STRUCTURE OF THE NEU/ERBB-2 MEMBRANE SPANNING SEGMENT -

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Basic information

Entry
Database: PDB / ID: 1iij
TitleSOLUTION STRUCTURE OF THE NEU/ERBB-2 MEMBRANE SPANNING SEGMENT
ComponentsERBB-2 RECEPTOR PROTEIN-TYROSINE KINASE
KeywordsSIGNALING PROTEIN / alpha-helix-pi-bulge-alpha-helix
Function / homology
Function and homology information


Signaling by ERBB2 / GRB7 events in ERBB2 signaling / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / GRB2 events in ERBB2 signaling / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / Downregulation of ERBB2 signaling / Sema4D induced cell migration and growth-cone collapse ...Signaling by ERBB2 / GRB7 events in ERBB2 signaling / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / GRB2 events in ERBB2 signaling / ERBB2 Regulates Cell Motility / PI3K events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / Downregulation of ERBB2 signaling / Sema4D induced cell migration and growth-cone collapse / SHC1 events in ERBB2 signaling / PIP3 activates AKT signaling / negative regulation of immature T cell proliferation in thymus / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / mammary gland involution / immature T cell proliferation in thymus / RNA polymerase I core binding / lateral loop / glial cell differentiation / sympathetic nervous system development / peripheral nervous system development / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / motor neuron axon guidance / positive regulation of Ras protein signal transduction / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / tongue development / ERBB2-EGFR signaling pathway / positive regulation of Rho protein signal transduction / neuromuscular junction development / ERBB2-ERBB3 signaling pathway / positive regulation of transcription by RNA polymerase I / regulation of cell differentiation / oligodendrocyte differentiation / microvillus / semaphorin-plexin signaling pathway / estrous cycle / positive regulation of cell adhesion / response to axon injury / positive regulation of protein targeting to membrane / coreceptor activity / Schwann cell development / skeletal muscle tissue development / cellular response to epidermal growth factor stimulus / myelination / transmembrane receptor protein tyrosine kinase activity / neurogenesis / basal plasma membrane / regulation of ERK1 and ERK2 cascade / liver development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to progesterone / positive regulation of translation / positive regulation of epithelial cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / Hsp90 protein binding / wound healing / neuromuscular junction / neuron differentiation / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / cellular response to growth factor stimulus / ruffle membrane / transmembrane signaling receptor activity / myelin sheath / presynaptic membrane / nervous system development / heart development / regulation of cell population proliferation / cytoplasmic vesicle / positive regulation of cell growth / basolateral plasma membrane / postsynaptic membrane / protein tyrosine kinase activity / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / cell surface receptor signaling pathway / receptor complex / endosome membrane / intracellular signal transduction / response to xenobiotic stimulus / apical plasma membrane / positive regulation of protein phosphorylation / protein heterodimerization activity / phosphorylation / signaling receptor binding / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / DNA binding / ATP binding
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 / 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
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
MethodSOLUTION NMR / molecular dynamics
AuthorsGoetz, M. / Carlotti, C. / Bontems, F. / Dufourc, E.J.
CitationJournal: Biochemistry / Year: 2001
Title: Evidence for an alpha-helix --> pi-bulge helicity modulation for the neu/erbB-2 membrane-spanning segment. A 1H NMR and circular dichroism study.
Authors: Goetz, M. / Carlotti, C. / Bontems, F. / Dufourc, E.J.
History
DepositionApr 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: ERBB-2 RECEPTOR PROTEIN-TYROSINE KINASE


Theoretical massNumber of molelcules
Total (without water)3,8951
Polymers3,8951
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)5 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ERBB-2 RECEPTOR PROTEIN-TYROSINE KINASE


Mass: 3894.845 Da / Num. of mol.: 1 / Fragment: TRANSMEMBRANE DOMAIN, RESIDUES 650-684 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. This sequence occurs naturally in Rattus norvegicus (rat).
References: UniProt: P06494, EC: 2.7.1.112

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
2212D NOESY
331HOHAHA

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Sample preparation

DetailsContents: 1.5 mM neu-tm35 peptide / Solvent system: deuterated TFE
Sample conditionsIonic strength: 0 / Pressure: ATMOSPHERIC atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE4001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionClassification
DYANAstructure solution
DiscoverVer. 97.0structure solution
XwinNMRcollection
DiscoverVer. 97.0refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Structures based 385 NOE restraints, 111 dihedral angles
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 5

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