[English] 日本語
Yorodumi
- PDB-1h9o: PHOSPHATIDYLINOSITOL 3-KINASE, P85-ALPHA SUBUNIT: C-TERMINAL SH2 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h9o
TitlePHOSPHATIDYLINOSITOL 3-KINASE, P85-ALPHA SUBUNIT: C-TERMINAL SH2 DOMAIN COMPLEXED WITH A TYR751 PHOSPHOPEPTIDE FROM THE PDGF RECEPTOR, CRYSTAL STRUCTURE AT 1.79 A
Components
  • BETA-PLATELET-DERIVED GROWTH FACTOR RECEPTOR
  • PHOSPHATIDYLINOSITOL 3-KINASEPhosphoinositide 3-kinase
KeywordsTRANSFERASE/RECEPTOR / COMPLEX (PHOSPHOTRANSFERASE-RECEPTOR) / PHOSPHOTRANSFERASE / SH2 DOMAIN / SIGNAL TRANSDUCTION / PHOSPHOINOSITIDE 3-KINASE / TRANSFERASE-RECEPTOR complex
Function / homology
Function and homology information


platelet activating factor receptor activity / platelet-derived growth factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / metanephric glomerular capillary formation / cell migration involved in vasculogenesis / aorta morphogenesis ...platelet activating factor receptor activity / platelet-derived growth factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / smooth muscle cell chemotaxis / metanephric glomerular capillary formation / cell migration involved in vasculogenesis / aorta morphogenesis / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / platelet-derived growth factor binding / retina vasculature development in camera-type eye / vascular endothelial growth factor binding / perinuclear endoplasmic reticulum membrane / cardiac myofibril assembly / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol metabolic process / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / positive regulation of chemotaxis / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / Signaling by PDGF / myeloid leukocyte migration / phosphatidylinositol 3-kinase regulatory subunit binding / 1-phosphatidylinositol-3-kinase regulator activity / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / cis-Golgi network / Activated NTRK3 signals through PI3K / kinase activator activity / ErbB-3 class receptor binding / RHOF GTPase cycle / transmembrane receptor protein tyrosine kinase adaptor activity / platelet-derived growth factor receptor binding / RHOD GTPase cycle / positive regulation of endoplasmic reticulum unfolded protein response / Signaling by cytosolic FGFR1 fusion mutants / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / RND2 GTPase cycle / MET activates PI3K/AKT signaling / PI3K/AKT activation / RND3 GTPase cycle / positive regulation of leukocyte migration / positive regulation of filopodium assembly / phosphatidylinositol 3-kinase complex, class IA / negative regulation of stress fiber assembly / growth hormone receptor signaling pathway / insulin binding / positive regulation of DNA biosynthetic process / RHOV GTPase cycle / RHOB GTPase cycle / Signaling by ALK / negative regulation of cell-matrix adhesion / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR2 / positive regulation of smooth muscle cell migration / PI-3K cascade:FGFR4 / RHOJ GTPase cycle / positive regulation of calcium ion import / RHOC GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / platelet-derived growth factor receptor-beta signaling pathway / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / positive regulation of phosphoprotein phosphatase activity / CDC42 GTPase cycle / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / PI3K events in ERBB2 signaling / Signaling by ALK fusions and activated point mutants / RHOG GTPase cycle / RET signaling / T cell differentiation / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / extrinsic apoptotic signaling pathway via death domain receptors / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / GAB1 signalosome / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / positive regulation of phospholipase C activity / positive regulation of lamellipodium assembly
Similarity search - Function
Platelet-derived growth factor receptor beta / 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 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Rho GTPase-activating protein domain ...Platelet-derived growth factor receptor beta / 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 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / 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 / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Platelet-derived growth factor receptor beta / Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsPauptit, R.A. / Rowsell, S. / Breeze, A.L. / Murshudov, G.N. / Dennis, C.A. / Derbyshire, D.J. / Weston, S.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: NMR Trial Models: Experiences with the Colicin Immunity Protein Im7 and the P85Alpha C-Terminal Sh2-Peptide Complex
Authors: Pauptit, R.A. / Dennis, C.A. / Derbyshire, D.J. / Breeze, A.L. / Weston, S.A. / Rowsell, S. / Murshudov, G.N.
History
DepositionMar 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-KINASE
B: BETA-PLATELET-DERIVED GROWTH FACTOR RECEPTOR


Theoretical massNumber of molelcules
Total (without water)13,3142
Polymers13,3142
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-10.74 kcal/mol
Surface area6130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.000, 32.800, 54.900
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number5
Space group name H-MC121
DetailsHETERODIMER CONSISTING OF P110 AND P85-ALPHA . THEC-TERMINAL SH2-DOMAIN (CHAIN A) IS A FRAGMENT OFP85-ALPHA. THE PENTAPEPTIDE (CHAIN B) IS A FRAGMENT OFPLATELET DERIVED GROWTH FACTOR RECEPTOR. CHAINSA AND B FORM A COMPLEX REPRESENTATIVE OF THEINTERACTION BETWEEN PI3 KINASE AND PDGF-RECEPTOR.

-
Components

#1: Protein PHOSPHATIDYLINOSITOL 3-KINASE / Phosphoinositide 3-kinase


Mass: 12612.094 Da / Num. of mol.: 1
Fragment: C-TERMINAL SH2 DOMAIN, P85-ALPHA REGULATORY SUBUNIT RESIDUES 617 - 724
Source method: isolated from a genetically manipulated source
Details: CONTAINS AN N-TERMINAL EXTENSION (GSPI) DERIVED FROM THE RECOMBINANT EXPRESSION VECTOR
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 (CGSC 6564) / References: UniProt: P27986
#2: Protein/peptide BETA-PLATELET-DERIVED GROWTH FACTOR RECEPTOR


Mass: 701.767 Da / Num. of mol.: 1 / Fragment: RESIDUES 751 - 755 / Source method: obtained synthetically / Details: TYROSINE-PHOSPHORYLATED PENTAPEPTIDE / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P09619
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPHOSPHATIDYLINOSITOL 3-KINASE ACTIVATES (PHOSPHORYLATED) PROTEIN-TYROSINE KINASES, THROUGH ITS SH2 DOMAIN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 43 % / Description: NMR TRIAL MODEL
Crystal growpH: 7
Details: 40MG/ML PROTEIN IN 20 MM PHOSPHATE PH6.2 + PEG8000, RESERVOIR WITH SAME PHOSPHATE + PEG8000 + 250MM NACL, pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→54 Å / Num. obs: 9283 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05
Reflection
*PLUS
Num. measured all: 36576

-
Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PIC

1pic


Resolution: 1.79→54 Å / SU B: 4.2 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.147 / Details: HYDROGENS ADDED IN RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 927 10 %RANDOM
Rwork0.163 ---
obs0.168 9283 93 %-
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.15 Å2
2--0.72 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.79→54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 0 110 1005
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.021
X-RAY DIFFRACTIONp_angle_d21.9
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.31.5
X-RAY DIFFRACTIONp_mcangle_it2.32
X-RAY DIFFRACTIONp_scbond_it2.93
X-RAY DIFFRACTIONp_scangle_it4.74.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1220.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg21.9

+
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