[English] 日本語
Yorodumi
- PDB-2k4p: Solution Structure of Ship2-Sam -

+
Open data


ID or keywords:

Loading...

-
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 / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / 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 / inositol-polyphosphate 5-phosphatase activity / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / 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 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / post-embryonic development / SH2 domain binding / basal plasma membrane / filopodium / actin filament organization / response to insulin / SH3 domain binding / spindle pole / Signaling by CSF1 (M-CSF) in myeloid cells / endocytosis / glucose metabolic process / lamellipodium / regulation of protein localization / 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 / Endonuclease/Exonuclease/phosphatase family 2 / 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 ...Transcription Factor, Ets-1 / Inositol polyphosphate-related phosphatase / Endonuclease/Exonuclease/phosphatase family 2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more