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- PDB-2lcx: Spatial Structure of the ErbB4 dimeric TM domain -

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Basic information

Entry
Database: PDB / ID: 2lcx
TitleSpatial Structure of the ErbB4 dimeric TM domain
ComponentsReceptor tyrosine-protein kinase erbB-4
KeywordsTRANSFERASE / tranmsembrane / helical dimer / dimerization / HER
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 / negative regulation of neuron migration / ERBB2-ERBB4 signaling pathway / mitochondrial fragmentation involved in apoptotic process ...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 / negative regulation of neuron migration / 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 / neural crest cell migration / epidermal growth factor receptor binding / positive regulation of tyrosine phosphorylation of STAT protein / neurotransmitter receptor localization to postsynaptic specialization membrane / ERBB2 Activates PTK6 Signaling / ERBB2 Regulates Cell Motility / Signaling by ERBB4 / Long-term potentiation / PI3K events in ERBB2 signaling / mammary gland alveolus development / SHC1 events in ERBB4 signaling / cell surface receptor signaling pathway via JAK-STAT / cell fate commitment / Nuclear signaling by ERBB4 / synapse assembly / positive regulation of cardiac muscle cell proliferation / Signaling by ERBB2 / transmembrane receptor protein tyrosine kinase activity / lactation / GRB2 events in ERBB2 signaling / Downregulation of ERBB4 signaling / SHC1 events in ERBB2 signaling / cellular response to epidermal growth factor stimulus / cell surface receptor protein tyrosine kinase signaling pathway / regulation of cell migration / positive regulation of epithelial cell proliferation / basal plasma membrane / GABA-ergic synapse / positive regulation of receptor signaling pathway via JAK-STAT / Signaling by ERBB2 TMD/JMD mutants / placental growth factor receptor activity / postsynaptic density membrane / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / neuromuscular junction / peptidyl-tyrosine phosphorylation / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / Downregulation of ERBB2 signaling / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / nervous system development / PIP3 activates AKT signaling / positive regulation of protein phosphorylation / presynaptic membrane / heart development / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein autophosphorylation / protein tyrosine kinase activity / basolateral plasma membrane / Estrogen-dependent gene expression / postsynaptic membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of ERK1 and ERK2 cascade / transcription cis-regulatory region binding / positive regulation of MAPK cascade / mitochondrial matrix / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / glutamatergic synapse / signal transduction / protein homodimerization activity / mitochondrion / extracellular region / nucleoplasm / 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 / 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-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMineev, K.S. / Bocharov, E.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
DepositionMay 11, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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
Water00
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 / Tyrosine kinase-type cell surface receptor HER4 / p180erbB4 ...Proto-oncogene-like protein c-ErbB-4 / Tyrosine kinase-type cell surface receptor HER4 / p180erbB4 / ERBB4 intracellular domain / 4ICD / E4ICD / s80HER4


Mass: 4769.830 Da / Num. of mol.: 2 / Fragment: Transmembrane residues 642-685
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB4, HER4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15303, receptor protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic
1913D (H)CCH-TOCSY
11013D 15N,13C-filtered, 13C-edited NOESY

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Sample preparation

DetailsContents: 1 mM protein, 1 mM [U-100% 13C; U-100% 15N] protein, 15 mM [U-2H] DMPC, 67 mM [U-2H] DHPC 1 mM sodium azide, 2 mM EDTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-11
1 mMprotein-2[U-100% 13C; U-100% 15N]1
15 mMDMPC-3[U-2H]1
67 mMDHPC-4[U-2H]1
1 mMsodium azide-51
2 mMEDTA-61
Sample conditionsIonic strength: 22 / pH: 5 / Pressure: ambient / 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
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CARA1.8.5Keller and Wuthrichchemical shift assignment
CARA1.8.5Keller and Wuthrichcollection
CARA1.8.5Keller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / 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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