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- PDB-2eao: Solution structure of the C-terminal SAM-domain of mouse ephrin t... -

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Basic information

Entry
Database: PDB / ID: 2eao
TitleSolution structure of the C-terminal SAM-domain of mouse ephrin type-B receptor 1 precursor (EC 2.7.1.112)
ComponentsEphrin type-B receptor 1
KeywordsSIGNALING PROTEIN / TRANSFERASE / CELL-FREE PROTEIN SYNTHESIS / PROTEIN REGULATION / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


skeletal muscle satellite cell activation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / negative regulation of satellite cell differentiation / central nervous system projection neuron axonogenesis / axon guidance receptor activity / immunological synapse formation / filopodium tip / dendritic spine development ...skeletal muscle satellite cell activation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / negative regulation of satellite cell differentiation / central nervous system projection neuron axonogenesis / axon guidance receptor activity / immunological synapse formation / filopodium tip / dendritic spine development / camera-type eye morphogenesis / dendritic spine morphogenesis / retinal ganglion cell axon guidance / EPH-Ephrin signaling / regulation of JNK cascade / positive regulation of synapse assembly / Ephrin signaling / neural precursor cell proliferation / establishment of cell polarity / cell-substrate adhesion / detection of temperature stimulus involved in sensory perception of pain / transmembrane-ephrin receptor activity / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of ERK1 and ERK2 cascade / neurogenesis / EPHB-mediated forward signaling / axon guidance / cell chemotaxis / receptor protein-tyrosine kinase / modulation of chemical synaptic transmission / protein autophosphorylation / early endosome membrane / angiogenesis / membrane raft / axon / dendrite / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B receptor 1, ligand binding domain / EphB1 , SAM domain / Transcription Factor, Ets-1 / 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 ...Ephrin type-B receptor 1, ligand binding domain / EphB1 , SAM domain / Transcription Factor, Ets-1 / 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 / Fibronectin type III domain / EGF-like domain signature 2. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / DNA polymerase; domain 1 / 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ephrin type-B receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A.K. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the C-terminal SAM-domain of mouse ephrin type-B receptor 1 precursor (EC 2.7.1.112)
Authors: Goroncy, A.K. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionJan 31, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 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 1.3May 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-B receptor 1


Theoretical massNumber of molelcules
Total (without water)10,5861
Polymers10,5861
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 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Ephrin type-B receptor 1 / Tyrosine-protein kinase receptor EPH-2 / NET / HEK6 / ELK


Mass: 10585.931 Da / Num. of mol.: 1 / Fragment: C-terminal SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: EPHB1, EPHT2, NET / Plasmid: P051003-03
References: UniProt: P54762, receptor protein-tyrosine kinase

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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: 1.14mM SAM DOMAIN; 20mM d-TRIS-HCL; 100mM NaCl; 1mM d-DTT; 0.02 % NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: AMBIENT / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.2P.GUNTERT ET AL.refinement
CYANA2.2.2P.GUNTERT ET AL.structure solution
XwinNMR3.5BRUKERcollection
NMRPipe20060702FRANK DELAGLIOprocessing
NMRView5.0.4BRUCE A. JOHNSONdata analysis
KUJIRA0.9821KOBAYASHI, N.data analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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