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- PDB-2k4p: Solution Structure of Ship2-Sam -

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Basic information

Entry
Database: PDB / ID: 2k4p
TitleSolution Structure of Ship2-Sam
ComponentsPhosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2
KeywordsSIGNALING PROTEIN / Helix bundle / Actin-binding / Alternative splicing / Cell adhesion / Cytoplasm / Cytoskeleton / Diabetes mellitus / Hydrolase / Immune response / Membrane / Phosphoprotein / Polymorphism / SH2 domain / SH3-binding
Function / homology
Function and homology information


negative regulation of insulin-like growth factor receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / ruffle assembly / regulation of actin filament organization / phosphatidylinositol dephosphorylation / endochondral ossification / phosphatidylinositol biosynthetic process / immune system process ...negative regulation of insulin-like growth factor receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / ruffle assembly / regulation of actin filament organization / phosphatidylinositol dephosphorylation / endochondral ossification / phosphatidylinositol biosynthetic process / immune system process / Synthesis of IP3 and IP4 in the cytosol / establishment of mitotic spindle orientation / Synthesis of PIPs at the plasma membrane / regulation of immune response / Interleukin receptor SHC signaling / ERK1 and ERK2 cascade / SH2 domain binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / basal plasma membrane / post-embryonic development / filopodium / actin filament organization / response to insulin / spindle pole / SH3 domain binding / endocytosis / glucose metabolic process / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of protein localization / lamellipodium / actin binding / gene expression / cell adhesion / nuclear speck / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / Golgi apparatus / nucleus / cytosol
Similarity search - Function
Transcription Factor, Ets-1 / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / 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 / SH2 domain ...Transcription Factor, Ets-1 / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLeone, M. / Pellecchia, M.
CitationJournal: Biochemistry / Year: 2008
Title: NMR Studies of a Heterotypic Sam-Sam Domain Association: The Interaction between the Lipid Phosphatase Ship2 and the EphA2 Receptor.
Authors: Leone, M. / Cellitti, J. / Pellecchia, M.
History
DepositionJun 16, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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: Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2


Theoretical massNumber of molelcules
Total (without water)9,5491
Polymers9,5491
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
RepresentativeModel #1fewest violations

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Components

#1: 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: 9548.537 Da / Num. of mol.: 1 / Fragment: Sterile alpha motif domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPPL1, SHIP2 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: O15357

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY
1332D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 15N] Ship2-Sam, 11.9 mM phosphates, 137 mM sodium chloride, 2.7 mM potassium chloride, 0.3% mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-100% 13C; U-100% 15N] Ship2-Sam, 11.9 mM phosphates, 137 mM sodium chloride, 2.7 mM potassium chloride, 0.3% mM sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.8 mM Ship2-Sam, 11.9 mM phosphates, 137 mM sodium chloride, 2.7 mM potassium chloride, 0.3% mM sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMShip2-Sam[U-100% 15N]1
11.9 mMphosphates1
137 mMsodium chloride1
2.7 mMpotassium chloride1
0.3 mMsodium azide1
0.8 mMShip2-Sam[U-100% 13C; U-100% 15N]2
11.9 mMphosphates2
137 mMsodium chloride2
2.7 mMpotassium chloride2
0.3 mMsodium azide2
0.8 mMShip2-Sam3
11.9 mMphosphates3
137 mMsodium chloride3
2.7 mMpotassium chloride3
0.3 mMsodium azide3
Sample conditionspH: 7.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospinprocessing
XEASYBartels, C. et al.data analysis
CYANA2.1Guntert, P. et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: This set of structures were generated by using only CYANA 2.1
NMR constraintsNOE constraints total: 989 / NOE intraresidue total count: 263 / NOE long range total count: 244 / NOE medium range total count: 242 / NOE sequential total count: 240
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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