[English] 日本語
Yorodumi
- PDB-1pht: PHOSPHATIDYLINOSITOL 3-KINASE P85-ALPHA SUBUNIT SH3 DOMAIN, RESID... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pht
TitlePHOSPHATIDYLINOSITOL 3-KINASE P85-ALPHA SUBUNIT SH3 DOMAIN, RESIDUES 1-85
ComponentsPHOSPHATIDYLINOSITOL 3-KINASE P85-ALPHA SUBUNIT
KeywordsPHOSPHOTRANSFERASE / PHOSPHATIDYLINOSITOL 3-KINASE / P85-ALPHA SUBUNIT / SH3 DOMAIN
Function / homology
Function and homology information


perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / positive regulation of focal adhesion disassembly / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulator activity / IRS-mediated signalling / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / positive regulation of focal adhesion disassembly / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulator activity / IRS-mediated signalling / positive regulation of endoplasmic reticulum unfolded protein response / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / T follicular helper cell differentiation / phosphatidylinositol 3-kinase complex / PI3K events in ERBB4 signaling / phosphatidylinositol 3-kinase regulatory subunit binding / myeloid leukocyte migration / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / cis-Golgi network / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / ErbB-3 class receptor binding / Signaling by cytosolic FGFR1 fusion mutants / Co-stimulation by ICOS / RHOD GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions / RHOF GTPase cycle / kinase activator activity / Signaling by LTK in cancer / positive regulation of leukocyte migration / Signaling by LTK / MET activates PI3K/AKT signaling / PI3K/AKT activation / negative regulation of stress fiber assembly / RND1 GTPase cycle / positive regulation of filopodium assembly / RND2 GTPase cycle / RND3 GTPase cycle / growth hormone receptor signaling pathway / insulin binding / Signaling by ALK / PI-3K cascade:FGFR3 / RHOV GTPase cycle / RHOB GTPase cycle / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / natural killer cell mediated cytotoxicity / GP1b-IX-V activation signalling / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / negative regulation of osteoclast differentiation / phosphatidylinositol phosphate biosynthetic process / Synthesis of PIPs at the plasma membrane / RHOU GTPase cycle / RET signaling / CDC42 GTPase cycle / PI3K events in ERBB2 signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / insulin receptor substrate binding / T cell differentiation / RHOG GTPase cycle / negative regulation of cell-matrix adhesion / extrinsic apoptotic signaling pathway via death domain receptors / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / Role of LAT2/NTAL/LAB on calcium mobilization / RAC2 GTPase cycle / RAC3 GTPase cycle / Interleukin receptor SHC signaling / Role of phospholipids in phagocytosis / GAB1 signalosome / enzyme-substrate adaptor activity / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / phosphatidylinositol 3-kinase binding / Signaling by FGFR4 in disease / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR3 in disease / Tie2 Signaling / insulin-like growth factor receptor binding / Signaling by FGFR2 in disease / phosphotyrosine residue binding / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / positive regulation of smooth muscle cell proliferation / Downstream signal transduction / substrate adhesion-dependent cell spreading / Interleukin-7 signaling / insulin-like growth factor receptor signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / osteoclast differentiation / response to endoplasmic reticulum stress
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 / SH3 Domains / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLiang, J. / Chen, J.K. / Schreiber, S.L. / Clardy, J.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of P13K SH3 domain at 20 angstroms resolution.
Authors: Liang, J. / Chen, J.K. / Schreiber, S.T. / Clardy, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: Structural Basis for the Binding of Proline-Rich Peptides to SH3 Domains
Authors: Yu, H. / Chen, J.K. / Dalgarno, D.C. / Brauer, A.W. / Schreiber, S.L.
History
DepositionAug 17, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-KINASE P85-ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)9,6311
Polymers9,6311
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.000, 47.000, 92.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 3 .. 85 SYMMETRY1 1 -1.000000 0.000000 0.000000 3.00000 SYMMETRY2 1 0.000000 1.000000 0.000000 1.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 3.00000 SYMMETRY1 2 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 2 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 2 0.000000 0.000000 -1.000000 1.00000

-
Components

#1: Protein PHOSPHATIDYLINOSITOL 3-KINASE P85-ALPHA SUBUNIT / PI3K SH3


Mass: 9630.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: NOVAGEN / Cell line: BL21(DE3) / Gene: PI3K SH3 FROM CDNA LIBRARY OF / Plasmid: PLM1-SH3 / Species (production host): Escherichia coli / Gene (production host): PI3K SH3 FROM CDNA LIBRARY OF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27986
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMprotein 1drop
210 mMTris-HCl1drop
3100 mMsodium phosphate1reservoir
41.4 Msodium citrate1reservoir
50.01 %sodium azide1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 16, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→8 Å / Num. obs: 6918 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.035
Reflection
*PLUS
% possible obs: 91 % / Observed criterion σ(I): 2 / Num. measured all: 32529 / Rmerge(I) obs: 0.032

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→8 Å / σ(F): 2
Details: SOLVENT MOLECULES WITH TEMPERATURE FACTORS GREATER THAN 50 ANGSTROMS**2 MAY NOT BE WELL DEFINED.
RfactorNum. reflection% reflection
Rfree0.258 --
Rwork0.223 --
obs0.223 6918 96 %
Displacement parametersBiso mean: 24.1 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 0 177 991
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.367
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.02
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.205
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.02
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.205

+
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