[English] 日本語
Yorodumi
- PDB-1qad: Crystal Structure of the C-Terminal SH2 Domain of the P85 alpha R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qad
TitleCrystal Structure of the C-Terminal SH2 Domain of the P85 alpha Regulatory Subunit of Phosphoinositide 3-Kinase: An SH2 domain mimicking its own substrate
ComponentsPI3-KINASE P85 ALPHA SUBUNIT
KeywordsTRANSFERASE / PHOPHOTYROSINE-BINDING DOMAIN / SUBSTRATE MIMICKING
Function / homology
Function and homology information


RHOC GTPase cycle / PI3K events in ERBB4 signaling / Interleukin-7 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / MET activates PI3K/AKT signaling / CDC42 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle ...RHOC GTPase cycle / PI3K events in ERBB4 signaling / Interleukin-7 signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / MET activates PI3K/AKT signaling / CDC42 GTPase cycle / RHOD GTPase cycle / RHOJ GTPase cycle / RAC3 GTPase cycle / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / FLT3 Signaling / RND2 GTPase cycle / RND1 GTPase cycle / IRS-mediated signalling / GPVI-mediated activation cascade / Signaling by SCF-KIT / Downstream signal transduction / PI3K/AKT activation / Signaling by ALK / Role of phospholipids in phagocytosis / Tie2 Signaling / Role of LAT2/NTAL/LAB on calcium mobilization / CD28 dependent PI3K/Akt signaling / RAC1 GTPase cycle / RAC2 GTPase cycle / Interleukin receptor SHC signaling / RND3 GTPase cycle / Co-stimulation by ICOS / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / PI3K Cascade / PIP3 activates AKT signaling / GP1b-IX-V activation signalling / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Synthesis of PIPs at the plasma membrane / RHOA GTPase cycle / RHOF GTPase cycle / DAP12 signaling / RHOU GTPase cycle / RHOV GTPase cycle / Regulation of signaling by CBL / Downstream TCR signaling / RHOG GTPase cycle / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase activator activity / phosphatidylinositol 3-kinase complex / transmembrane receptor protein tyrosine kinase adaptor activity / ErbB-3 class receptor binding / phosphatidylinositol 3-kinase complex, class IA / Extra-nuclear estrogen signaling / G alpha (q) signalling events / phosphatidylinositol phosphate biosynthetic process / intracellular glucose homeostasis / insulin receptor substrate binding / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase binding / insulin-like growth factor receptor binding / substrate adhesion-dependent cell spreading / insulin-like growth factor receptor signaling pathway / response to endoplasmic reticulum stress / positive regulation of RNA splicing / positive regulation of D-glucose import / insulin receptor binding / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein import into nucleus / cellular response to insulin stimulus / insulin receptor signaling pathway / protein transport / protein stabilization / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsHoedemaeker, P.J. / Siegal, G. / Roe, M. / Driscoll, P.C. / Abrahams, J.P.A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the C-terminal SH2 domain of the p85alpha regulatory subunit of phosphoinositide 3-kinase: an SH2 domain mimicking its own substrate.
Authors: Hoedemaeker, F.J. / Siegal, G. / Roe, S.M. / Driscoll, P.C. / Abrahams, J.P.
History
DepositionFeb 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PI3-KINASE P85 ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)12,6151
Polymers12,6151
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.680, 46.920, 62.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PI3-KINASE P85 ALPHA SUBUNIT


Mass: 12615.052 Da / Num. of mol.: 1 / Fragment: C-TERMINAL SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P23727
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.427 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 277 K / Method: spontaneous crystallisation / pH: 7.5
Details: TRIS-HCL, NACL, EDTA, DTT, pH 7.5, SPONTANEOUS CRYSTALLISATION, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
11mM protein (~13mg/ml)11
250mM TRIS-HCL12
350mM NaCl12
41mM DTT12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Eck, M.J., (1993) Nature, 362, 87. / pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125-35 %PEG20001reservoircan be replaced by PEG4000 or PEG8000
250 mM1reservoirMgCl2
3100 mMsodium acetate1reservoirpH4.6
450 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→23.44 Å / Num. all: 10947 / Num. obs: 10947 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 18 Å2 / Net I/σ(I): 7.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3 % / Mean I/σ(I) obs: 10.2 / % possible all: 84.5
Reflection
*PLUS
Num. measured all: 37237 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 84.5 % / Num. unique obs: 677 / Num. measured obs: 2058 / Rmerge(I) obs: 0.068

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
WARPmodel building
REFMACrefinement
CCP4(SCALA)data scaling
ARP/wARPmodel building
RefinementStarting model: 1BFJ

1bfj


Resolution: 1.8→23.44 Å / SU B: 2.3668 / SU ML: 0.07628 / Cross valid method: Rfree / ESU R Free: 0.14209 / Stereochemistry target values: ENGH & HUBER
Details: CONJUGATED DIRECTION METHOD WITH MAXIMUM LIKELYHOOD TARGET (REFMAC_aniso)
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1121 -RANDOM
Rwork0.158 ---
all-10947 --
obs-9826 88.6 %-
Refinement stepCycle: LAST / Resolution: 1.8→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 0 185 1015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / Rfactor Rfree: 0.231 / Num. reflection Rfree: 135 / Num. reflection Rwork: 1159 / Rfactor obs: 0.118

+
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