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- PDB-2kso: EphA2:SHIP2 SAM:SAM complex -

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Basic information

Entry
Database: PDB / ID: 2kso
TitleEphA2:SHIP2 SAM:SAM complex
Components
  • Ephrin type-A receptor 2
  • Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2
KeywordsPROTEIN BINDING / SAM domain / heterodimer / cell signaling / Angiogenesis / Apoptosis / ATP-binding / Cataract / Disulfide bond / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transferase / Transmembrane / Tyrosine-protein kinase / Actin-binding / Cell adhesion / Cytoskeleton / Diabetes mellitus / Hydrolase / Immune response / SH2 domain / SH3-binding
Function / homology
Function and homology information


negative regulation of insulin-like growth factor receptor signaling pathway / notochord cell development / notochord formation / inositol-polyphosphate 5-phosphatase activity / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / lens fiber cell morphogenesis / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / axial mesoderm formation ...negative regulation of insulin-like growth factor receptor signaling pathway / notochord cell development / notochord formation / inositol-polyphosphate 5-phosphatase activity / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / lens fiber cell morphogenesis / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / axial mesoderm formation / ruffle assembly / cAMP metabolic process / regulation of blood vessel endothelial cell migration / pericyte cell differentiation / phosphatidylinositol dephosphorylation / leading edge membrane / regulation of actin filament organization / negative regulation of chemokine production / ephrin receptor activity / endochondral ossification / activation of GTPase activity / post-anal tail morphogenesis / response to growth factor / phosphatidylinositol biosynthetic process / positive regulation of bicellular tight junction assembly / bone remodeling / regulation of lamellipodium assembly / negative regulation of cell adhesion mediated by integrin / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / central nervous system neuron differentiation / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / neural tube development / mammary gland epithelial cell proliferation / tight junction / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / establishment of mitotic spindle orientation / Synthesis of IP3 and IP4 in the cytosol / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / lamellipodium membrane / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC3 GTPase cycle / RAC2 GTPase cycle / regulation of angiogenesis / Interleukin receptor SHC signaling / ephrin receptor signaling pathway / regulation of immune response / immune system process / vasculogenesis / regulation of ERK1 and ERK2 cascade / keratinocyte differentiation / ERK1 and ERK2 cascade / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / osteoclast differentiation / SH2 domain binding / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / negative regulation of angiogenesis / molecular function activator activity / actin filament organization / protein localization to plasma membrane / post-embryonic development / positive regulation of protein localization to plasma membrane / cell chemotaxis / skeletal system development / filopodium / cell motility / phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor protein-tyrosine kinase / response to insulin / SH3 domain binding / glucose metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage / ruffle membrane / endocytosis / spindle pole / Signaling by CSF1 (M-CSF) in myeloid cells / osteoblast differentiation / regulation of protein localization / cell migration / lamellipodium / virus receptor activity / actin binding / angiogenesis / gene expression / cell adhesion / signaling receptor complex / nuclear speck / defense response to Gram-positive bacterium / positive regulation of cell migration / cadherin binding / inflammatory response / negative regulation of cell population proliferation
Similarity search - Function
Ephrin type-A receptor 2, ligand binding domain / : / : / SHIP1/2 second C2 domain / SHIP1/2 first C2 domain / Transcription Factor, Ets-1 / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues / Ephrin cysteine rich domain ...Ephrin type-A receptor 2, ligand binding domain / : / : / SHIP1/2 second C2 domain / SHIP1/2 first C2 domain / Transcription Factor, Ets-1 / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / Inositol polyphosphate phosphatase, catalytic domain homologues / Ephrin cysteine rich 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 / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / Endonuclease/exonuclease/phosphatase superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type 3 domain / SH2 domain / Galactose-binding-like domain superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain 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
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsHota, P.K. / Preeti, C. / Stetzik, L. / Kim, S. / Wang, B. / Lee, H. / Buck, M.
CitationJournal: To be Published
Title: Structure and function of the EphA2:SHIP2 SAM domain heterodimer
Authors: Lee, H. / Hota, P. / Preeti, C. / Wang, B. / Buck, M.
History
DepositionJan 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ephrin type-A receptor 2
B: Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2


Theoretical massNumber of molelcules
Total (without water)18,0732
Polymers18,0732
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)15 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Ephrin type-A receptor 2 / Tyrosine-protein kinase receptor ECK / Epithelial cell kinase


Mass: 9401.755 Da / Num. of mol.: 1 / Fragment: EphA2 SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: P29317
#2: Protein Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2 / SH2 domain-containing inositol-5'-phosphatase 2 / SHIP-2 / Inositol polyphosphate phosphatase-like ...SH2 domain-containing inositol-5'-phosphatase 2 / SHIP-2 / Inositol polyphosphate phosphatase-like protein 1 / INPPL-1 / Protein 51C


Mass: 8671.604 Da / Num. of mol.: 1 / Fragment: SHIP2 SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPPL1, SHIP2 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: O15357

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR Solution structure of SAM Domain Heterodimer
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-15N NOESY
NMR detailsText: full list to be completed

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] entity_1-1, 0.9 mM entity_2-2, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM entity_1-3, 0.6 mM [U-100% 13C; U-100% 15N] entity_2-4, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMentity_1-1[U-100% 13C; U-100% 15N]1
0.9 mMentity_2-21
0.9 mMentity_1-32
0.6 mMentity_2-4[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient atm / Temperature: 300 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 softwareName: X-PLOR NIH / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: standard protocol
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 15

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