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- PDB-2jwa: ErbB2 transmembrane segment dimer spatial structure -

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Basic information

Entry
Database: PDB / ID: 2jwa
TitleErbB2 transmembrane segment dimer spatial structure
ComponentsReceptor tyrosine-protein kinase erbB-2
KeywordsTRANSFERASE / transmembrane helix dimer / ErbB2 / protein kinase receptor membrane domain / ATP-binding / Glycoprotein / Nucleotide-binding / Phosphorylation / Polymorphism / Tyrosine-protein kinase
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 / 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 / positive regulation of transcription by RNA polymerase I / 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 / Schwann cell development / coreceptor activity / 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 / SHC1 events in ERBB2 signaling / positive regulation of cell adhesion / Constitutive Signaling by Overexpressed ERBB2 / Downregulation of ERBB2:ERBB3 signaling / regulation of ERK1 and ERK2 cascade / basal plasma membrane / neurogenesis / positive regulation of epithelial cell proliferation / positive regulation of translation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / neuromuscular junction / receptor protein-tyrosine kinase / neuron differentiation / receptor tyrosine kinase binding / cellular response to growth factor stimulus / Downregulation of ERBB2 signaling / ruffle membrane / peptidyl-tyrosine phosphorylation / 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 / positive regulation of cell growth / basolateral plasma membrane / protein tyrosine kinase activity / positive regulation of MAPK cascade / early endosome / receptor complex / cell surface receptor signaling pathway / endosome membrane / intracellular signal transduction / positive regulation of protein phosphorylation / protein heterodimerization activity / apical plasma membrane / protein phosphorylation / 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
Cytochrome c1, transmembrane anchor, C-terminal / : / 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 ...Cytochrome c1, transmembrane anchor, C-terminal / : / 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 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsstructure of dimer of transmembrane segments of receptor tyrosine kinase ErbB2
AuthorsMineev, K.S. / Bocharov, E.V. / Arseniev, A.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Spatial Structure of the Dimeric Transmembrane Domain of the Growth Factor Receptor ErbB2 Presumably Corresponding to the Receptor Active State
Authors: Bocharov, E.V. / Mineev, K.S. / Volynsky, P.E. / Ermolyuk, Y.S. / Tkach, E.N. / Sobol, A.G. / Chupin, V.V. / Kirpichnikov, M.P. / Efremov, R.G. / Arseniev, A.S.
History
DepositionOct 9, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 100target function
RepresentativeModel #1fewest violations

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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 ...p185erbB2 / C-erbB-2 / NEU proto-oncogene / Tyrosine kinase-type cell surface receptor HER2 / MLN 19 / CD340 antigen


Mass: 4734.805 Da / Num. of mol.: 2 / Fragment: 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: structure of dimer of transmembrane segments of receptor tyrosine kinase ErbB2
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-15N TOCSY
1523D 1H-13C NOESY
1623D (H)CCH-TOCSY
1723D HNCA
1823D HN(CO)CA
1913D HNHA
11013D HNHB
11133D-C13-CHIRP-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0mM [U-15N] ErbB2, 64mM [U-2H] DHPC, 16mM [U-2H] DMPC, 95% H2O/5% D2O95% H2O/5% D2O
22.0mM [U-13C; U-15N] ErbB2, 64mM [U-2H] DHPC, 16mM [U-2H] DMPC, 95% H2O/5% D2O95% H2O/5% D2O
31.0mM [U-13C; U-15N] ErbB2, 64mM [U-2H] DHPC, 16mM [U-2H] DMPC, 1.0mM ErbB2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMErbB2[U-15N]1
64 mMDHPC[U-2H]1
16 mMDMPC[U-2H]1
2.0 mMErbB2[U-13C; U-15N]2
64 mMDHPC[U-2H]2
16 mMDMPC[U-2H]2
1.0 mMErbB2[U-13C; U-15N]3
64 mMDHPC[U-2H]3
16 mMDMPC[U-2H]3
Sample conditionspH: 5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CARA1.8.3Wutrich, Kellerchemical shift assignment
CARA1.8.3Wutrich, Kellerdata analysis
GROMACS3.2.1Lindahl E, Hess D, Van der Spoel B.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 100 structures was annealed, 12 structures were deposited.
NMR constraintsNOE constraints total: 594 / NOE intraresidue total count: 186 / NOE long range total count: 22 / NOE medium range total count: 250 / NOE sequential total count: 136 / Hydrogen bond constraints total count: 3 / Protein chi angle constraints total count: 40 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 56 / Protein psi angle constraints total count: 56
NMR representativeSelection criteria: fewest violations
NMR ensembleAverage torsion angle constraint violation: 0.04 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 12 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0.27 ° / Maximum upper distance constraint violation: 0.09 Å
NMR ensemble rmsDistance rms dev: 0.01 Å / Distance rms dev error: 0.001 Å

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