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- PDB-2k1l: NMR structures of dimeric transmembrane domain of the receptor ty... -

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Basic information

Entry
Database: PDB / ID: 2k1l
TitleNMR structures of dimeric transmembrane domain of the receptor tyrosine kinase EphA1 in lipid bicelles at pH 6.3
ComponentsEphrin type-A receptor 1
KeywordsSIGNALING PROTEIN / EphA1 / receptor tyrosine kinase / dimeric transmembrane domain / ATP-binding / Glycoprotein / Nucleotide-binding / Phosphoprotein / Polymorphism / Transferase / Tyrosine-protein kinase
Function / homology
Function and homology information


POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / transmembrane-ephrin receptor activity / activation of GTPase activity / EPH-Ephrin signaling / positive regulation of cell-matrix adhesion / regulation of GTPase activity / EPHA-mediated growth cone collapse / fibronectin binding / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / transmembrane-ephrin receptor activity / activation of GTPase activity / EPH-Ephrin signaling / positive regulation of cell-matrix adhesion / regulation of GTPase activity / EPHA-mediated growth cone collapse / fibronectin binding / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / positive regulation of stress fiber assembly / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / negative regulation of cell migration / negative regulation of protein kinase activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / angiogenesis / protein autophosphorylation / cell surface receptor signaling pathway / receptor complex / protein kinase activity / positive regulation of cell migration / positive regulation of cell population proliferation / protein kinase binding / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 1, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. ...Ephrin type-A receptor 1, ligand binding domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Ephrin type-A receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMayzel, M.L. / Bocharov, E.V. / Arseniev, A.S. / Goncharuk, M.V.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Spatial Structure and pH-dependent Conformational Diversity of Dimeric Transmembrane Domain of the Receptor Tyrosine Kinase EphA1.
Authors: Bocharov, E.V. / Mayzel, M.L. / Volynsky, P.E. / Goncharuk, M.V. / Ermolyuk, Y.S. / Schulga, A.A. / Artemenko, E.O. / Efremov, R.G. / Arseniev, A.S.
History
DepositionMar 7, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 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: Ephrin type-A receptor 1
B: Ephrin type-A receptor 1


Theoretical massNumber of molelcules
Total (without water)7,7892
Polymers7,7892
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)12 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Ephrin type-A receptor 1 / Tyrosine-protein kinase receptor EPH


Mass: 3894.700 Da / Num. of mol.: 2 / Fragment: Transmembrane region, UNP residue 536-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA1, EPH, EPHT, EPHT1 / Production host: Escherichia coli (E. coli)
References: UniProt: P21709, receptor protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1323D 1H-15N NOESY
1413D 1H-13C NOESY
15313C F1-filtered/F3-edited-NOESY
16215N-T1
17215N-T2
18215N-NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mM 15N, 13C EphA1_TM 15N, 13C, 96 mM 2H DHPC, 24 mM 2H DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer, 100% D2O100% D2O
23 mM 15N, 13C EphA1_TM 15N, 96 mM 2H DHPC, 24 mM 2H DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer, 95% H2O/5% D2O95% H2O/5% D2O
31.5 mM 15N, 13C EphA1_TM 15N,13C, 96 mM 2H DHPC, 24 mM 2H DMPC, 1.5 mM NaN3, 1 mM EDTA, 10 mM phosphate buffer, 1.5 mM EphA1_TM, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMEphA1_TM 15N,13C15N, 13C1
96 mMDHPC2H1
24 mMDMPC2H1
1.5 uMNaN31
1 mMEDTA1
10 mMphosphate buffer1
3 mMEphA1_TM 15N15N, 13C2
96 mMDHPC2H2
24 mMDMPC2H2
1.5 uMNaN32
1 mMEDTA2
10 mMphosphate buffer2
1.5 mMEphA1_TM 15N,13C15N, 13C3
96 mMDHPC2H3
24 mMDMPC2H3
1.5 uMNaN33
1 mMEDTA3
10 mMphosphate buffer3
1.5 mMEphA1_TM3
Sample conditionspH: 6.3 / 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
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.5.5, 1.8Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 12

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