[English] 日本語
Yorodumi
- PDB-1fu6: NMR STRUCTURE OF THE N-SH2 DOMAIN OF THE P85 SUBUNIT OF PI3-KINASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fu6
TitleNMR STRUCTURE OF THE N-SH2 DOMAIN OF THE P85 SUBUNIT OF PI3-KINASE
ComponentsPHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT
KeywordsPROTEIN BINDING / central beta-sheet with two flanking alpha-helices
Function / homology
Function and homology information


PI3K events in ERBB4 signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Costimulation by the CD28 family / CD28 dependent PI3K/Akt signaling / MET activates PI3K/AKT signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin receptor SHC signaling / Tie2 Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / FLT3 Signaling ...PI3K events in ERBB4 signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Costimulation by the CD28 family / CD28 dependent PI3K/Akt signaling / MET activates PI3K/AKT signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Interleukin receptor SHC signaling / Tie2 Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / FLT3 Signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / RHOJ GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / IRS-mediated signalling / Interleukin-7 signaling / GP1b-IX-V activation signalling / GPVI-mediated activation cascade / Synthesis of PIPs at the plasma membrane / PI3K/AKT activation / PI-3K cascade:FGFR2 / Regulation of signaling by CBL / Downstream TCR signaling / RHOF GTPase cycle / PI3K Cascade / VEGFA-VEGFR2 Pathway / Signaling by SCF-KIT / RHOB GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RND3 GTPase cycle / PIP3 activates AKT signaling / Downstream signal transduction / Signaling by ALK / RHOG GTPase cycle / Role of phospholipids in phagocytosis / RAC2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / DAP12 signaling / RAC1 GTPase cycle / RET signaling / RHOA GTPase cycle / Extra-nuclear estrogen signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / perinuclear endoplasmic reticulum membrane / response to yeast / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol metabolic process / negative regulation of muscle cell apoptotic process / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / response to fatty acid / interleukin-18-mediated signaling pathway / myeloid leukocyte migration / response to fructose / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / cis-Golgi network / response to growth factor / ErbB-3 class receptor binding / negative regulation of cell adhesion / kinase activator activity / regulation of stress fiber assembly / platelet-derived growth factor receptor binding / positive regulation of endoplasmic reticulum unfolded protein response / G alpha (q) signalling events / phosphatidylinositol 3-kinase complex, class IA / response to iron(II) ion / positive regulation of synapse assembly / RAF/MAP kinase cascade / phosphatidylinositol 3-kinase complex / positive regulation of leukocyte migration / positive regulation of filopodium assembly / negative regulation of stress fiber assembly / growth hormone receptor signaling pathway / cellular response to fatty acid / insulin binding / negative regulation of heart rate / 1-phosphatidylinositol-3-kinase activity / negative regulation of cell-matrix adhesion / negative regulation of cell-cell adhesion / response to testosterone / response to dexamethasone / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / phosphatidylinositol phosphate biosynthetic process / extrinsic apoptotic signaling pathway via death domain receptors / insulin receptor substrate binding / positive regulation of myoblast differentiation / response to amino acid / regulation of protein localization to plasma membrane / positive regulation of lamellipodium assembly / response to glucocorticoid
Similarity search - Function
Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases ...Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / The structures were energy minimized with MSI DISCOVER.
AuthorsWeber, T. / Schaffhausen, B. / Liu, Y. / Guenther, U.L.
CitationJournal: Biochemistry / Year: 2000
Title: NMR structure of the N-SH2 of the p85 subunit of phosphoinositide 3-kinase complexed to a doubly phosphorylated peptide reveals a second phosphotyrosine binding site.
Authors: Weber, T. / Schaffhausen, B. / Liu, Y. / Gunther, U.L.
History
DepositionSep 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)12,8701
Polymers12,8701
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 110structures with favorable non-bond energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY ALPHA SUBUNIT / N-SH2 (SRC HOMOLOGY 2) DOMAIN OF P85 SUBUNIT OF P13-KINASE (PHOSPHOINOSITOL 3-KINASE) / PI3-KINASE ...N-SH2 (SRC HOMOLOGY 2) DOMAIN OF P85 SUBUNIT OF P13-KINASE (PHOSPHOINOSITOL 3-KINASE) / PI3-KINASE P85-ALPHA SUBUNIT / PTDINS-3-KINASE P85-ALPHA / PI3K


Mass: 12870.384 Da / Num. of mol.: 1
Fragment: RESIDUES 321 TO 431 OF P85, N-SH2 (SRC HOMOLOGY 2) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q63787

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D NOESY
NMR detailsText: NOESY assignments were obtained by a semi-automatic procedure employing a program from Pristovsek [Pristovsek, P. & Kidric, J. (1997) Biopol. 42, 671-679)].

-
Sample preparation

DetailsContents: 1.5mM N-SH2 15N, 13C; 0.1mM KCl; 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 0.1mM / pH: 6.8 / Pressure: 1 bar / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

-
Processing

NMR software
NameDeveloperClassification
NMRLABUlrich Guenther, Christian Ludwig and Heinz Rueterjansprocessing
ProntoM. Kjaerdata analysis
nmr2stP. Pristovsekdata analysis
DYANAP. Guentertstructure solution
DiscoverMSIrefinement
RefinementMethod: The structures were energy minimized with MSI DISCOVER.
Software ordinal: 1 / Details: The structure with the lowest energy is presented.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 110 / Conformers submitted total number: 1

+
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