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- PDB-2l2t: Solution NMR structure of the ErbB4 dimeric membrane domain -

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Basic information

Entry
Database: PDB / ID: 2l2t
TitleSolution NMR structure of the ErbB4 dimeric membrane domain
ComponentsReceptor tyrosine-protein kinase erbB-4
KeywordsMEMBRANE PROTEIN / ErbB4 / transmembrane dimer / membrane domain
Function / homology
Function and homology information


establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / neuregulin receptor activity / cardiac muscle tissue regeneration / ERBB2-ERBB4 signaling pathway / mitochondrial fragmentation involved in apoptotic process / GABA receptor binding ...establishment of planar polarity involved in nephron morphogenesis / ERBB4 signaling pathway / ERBB4-ERBB4 signaling pathway / olfactory bulb interneuron differentiation / central nervous system morphogenesis / neuregulin receptor activity / cardiac muscle tissue regeneration / ERBB2-ERBB4 signaling pathway / mitochondrial fragmentation involved in apoptotic process / GABA receptor binding / PI3K events in ERBB4 signaling / mammary gland epithelial cell differentiation / embryonic pattern specification / positive regulation of protein localization to cell surface / neurotransmitter receptor localization to postsynaptic specialization membrane / neural crest cell migration / epidermal growth factor receptor activity / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / cell surface receptor signaling pathway via JAK-STAT / Long-term potentiation / PI3K events in ERBB2 signaling / SHC1 events in ERBB4 signaling / GABA-ergic synapse / mammary gland alveolus development / cell fate commitment / Nuclear signaling by ERBB4 / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of cardiac muscle cell proliferation / regulation of cell migration / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / synapse assembly / Downregulation of ERBB4 signaling / lactation / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / neurogenesis / basal plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / postsynaptic density membrane / Signaling by ERBB2 TMD/JMD mutants / positive regulation of receptor signaling pathway via JAK-STAT / neuromuscular junction / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / presynaptic membrane / nervous system development / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / basolateral plasma membrane / postsynaptic membrane / protein tyrosine kinase activity / Estrogen-dependent gene expression / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / transcription cis-regulatory region binding / mitochondrial matrix / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / glutamatergic synapse / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / signal transduction / protein homodimerization activity / mitochondrion / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #880 / : / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #880 / : / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Helix non-globular / Special / 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-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsMineev, K.S. / Bocharov, E.V. / Goncharuk, M.V. / Arseniev, A.S.
CitationJournal: Biochim. Biophys. Acta / Year: 2012
Title: Structural and thermodynamic insight into the process of "weak" dimerization of the ErbB4 transmembrane domain by solution NMR.
Authors: Bocharov, E.V. / Mineev, K.S. / Goncharuk, M.V. / Arseniev, A.S.
History
DepositionAug 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
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_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-4
B: Receptor tyrosine-protein kinase erbB-4


Theoretical massNumber of molelcules
Total (without water)9,5402
Polymers9,5402
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)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Receptor tyrosine-protein kinase erbB-4 / Proto-oncogene-like protein c-ErbB-4 / p180erbB4 / Tyrosine kinase-type cell surface receptor HER4


Mass: 4769.830 Da / Num. of mol.: 2 / Fragment: membrane domain (UNP RESIDUES 642-685)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB4, HER4 / Plasmid: pGemex1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS
References: UniProt: Q15303, receptor protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution NMR structure of the ErbB4 dimeric membrane domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D HN(CO)CA
1612D 1H-1H NOESY
1713D 1H-15N NOESY
1833D (H)CCH-TOCSY
1933D 1H-13C NOESY
11033D 13C-filt. NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-98% 15N] protein, 10 mM EDTA, 2 mM sodium azide, 12 mM DMPC, 48 mM DHPC, 90% H2O/10% D2O90% H2O/10% D2O
21 mM protein, 10 mM EDTA, 2 mM sodium azide, 12 mM DMPC, 48 mM DHPC, 1 mM [U-98% 13C; U-98% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
31 mM protein, 10 mM EDTA, 2 mM sodium azide, 12 mM DMPC, 48 mM DHPC, 1 mM [U-98% 13C; U-98% 15N] protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity-1[U-98% 15N]1
10 mMEDTA-21
2 mMsodium azide-31
12 mMDMPC-41
48 mMDHPC-51
1 mMentity-62
10 mMEDTA-72
2 mMsodium azide-82
12 mMDMPC-92
48 mMDHPC-102
1 mMentity-11[U-98% 13C; U-98% 15N]2
1 mMentity-123
10 mMEDTA-133
2 mMsodium azide-143
12 mMDMPC-153
48 mMDHPC-163
1 mMentity-17[U-98% 13C; U-98% 15N]3
Sample conditionsIonic strength: 20 / pH: 5.0 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian UnityVarianUNITY6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CARA1.8.3Keller and Wuthrichchemical shift assignment
CARA1.8.3Keller and Wuthrichdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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