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- PDB-1sgg: THE SOLUTION STRUCTURE OF SAM DOMAIN FROM THE RECEPTOR TYROSINE K... -

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Basic information

Entry
Database: PDB / ID: 1sgg
TitleTHE SOLUTION STRUCTURE OF SAM DOMAIN FROM THE RECEPTOR TYROSINE KINASE EPHB2, NMR, 10 STRUCTURES
ComponentsEPHRIN TYPE-B RECEPTOR 2
KeywordsTYROSINE-PROTEIN KINASE / RECEPTOR OLIGOMERIZATION / EPH RECEPTORS / TYROSINE PHOSPHORYLATION / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


spinothalamic tract morphogenesis / central nervous system projection neuron axonogenesis / multicellular organism development / dendritic spine development / transmembrane-ephrin receptor activity / dendritic spine morphogenesis / positive regulation of kinase activity / axonal fasciculation / positive regulation of synapse assembly / plasma membrane => GO:0005886 ...spinothalamic tract morphogenesis / central nervous system projection neuron axonogenesis / multicellular organism development / dendritic spine development / transmembrane-ephrin receptor activity / dendritic spine morphogenesis / positive regulation of kinase activity / axonal fasciculation / positive regulation of synapse assembly / plasma membrane => GO:0005886 / ephrin receptor signaling pathway / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / axon guidance / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / protein tyrosine kinase activity / angiogenesis / receptor complex / neuron projection / axon / dendrite / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-B receptor 2, ligand binding domain / Transcription Factor, Ets-1 / 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 ...Ephrin type-B receptor 2, ligand binding domain / Transcription Factor, Ets-1 / 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 / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ephrin type-B receptor 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing
AuthorsSmalla, M. / Schmieder, P. / Kelly, M. / Ter Laak, A. / Krause, G. / Ball, L. / Wahl, M. / Bork, P. / Oschkinat, H.
CitationJournal: Protein Sci. / Year: 1999
Title: Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites.
Authors: Smalla, M. / Schmieder, P. / Kelly, M. / Ter Laak, A. / Krause, G. / Ball, L. / Wahl, M. / Bork, P. / Oschkinat, H.
History
DepositionJan 8, 1999Processing site: BNL
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 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 2


Theoretical massNumber of molelcules
Total (without water)8,5401
Polymers8,5401
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)10 / 200LOWEST ENERGIES
RepresentativeModel #1

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Components

#1: Protein EPHRIN TYPE-B RECEPTOR 2


Mass: 8539.660 Da / Num. of mol.: 1 / Fragment: SAM DOMAIN
Source method: isolated from a genetically manipulated source
Details: POTENTIAL TYROSINE PHOSPHORYLATION AT Y 25 / Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PET 28D / Cell line (production host): BL21 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Tissue (production host): EMBRYO / References: UniProt: P28693, 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
1112D-NOESY
1212D-TOCSY
1311H-15 NOESY
1411H-13C NOESY
151(H)CCH-TOCSY
161(H)CCH-COSY
171CBCANNH
181CBCA (CO)NNH
191CC(CO)NNH-TOCSY
1101HBHA(CO)NNH
1111HC(CO)NNH-TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED EPHB2 SAM DOMAIN

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Sample preparation

DetailsContents: 100% H2O
Sample conditionspH: 5.8 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX600BrukerDRX6006001
Bruker DRX750BrukerDRX7507502

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGIES / Conformers calculated total number: 200 / Conformers submitted total number: 10

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