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- PDB-1x5a: The solution structure of the second fibronectin type III domain ... -

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Entry
Database: PDB / ID: 1x5a
TitleThe solution structure of the second fibronectin type III domain of mouse Ephrin type-A receptor 1
ComponentsEphrin type-A receptor 1
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Tyrosine-protein kinase receptor / ESK / fibronectin type III (fn3) domain / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


EPH-Ephrin signaling / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor activity / transmembrane-ephrin receptor activity / positive regulation of kinase activity / activation of GTPase activity / positive regulation of cell-matrix adhesion / regulation of GTPase activity / plasma membrane => GO:0005886 ...EPH-Ephrin signaling / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor activity / transmembrane-ephrin receptor activity / positive regulation of kinase activity / activation of GTPase activity / positive regulation of cell-matrix adhesion / regulation of GTPase activity / plasma membrane => GO:0005886 / fibronectin binding / positive regulation of stress fiber assembly / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / negative regulation of cell migration / substrate adhesion-dependent cell spreading / axon guidance / 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 / neuron projection / positive regulation of cell population proliferation / protein kinase binding / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 1, ligand binding domain / 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 type-A receptor 1, ligand binding domain / 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 / 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 / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ephrin type-A receptor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTochio, N. / Sasagawa, A. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: The solution structure of the second fibronectin type III domain of mouse Ephrin type-A receptor 1
Authors: Tochio, N. / Sasagawa, A. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4May 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


Theoretical massNumber of molelcules
Total (without water)11,6741
Polymers11,6741
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 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 11674.067 Da / Num. of mol.: 1 / Fragment: Fibronectin type-III domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Epha1 / Plasmid: P040719-10 / References: UniProt: Q60750, 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
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.2mM FN3 domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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