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- PDB-1h9o: PHOSPHATIDYLINOSITOL 3-KINASE, P85-ALPHA SUBUNIT: C-TERMINAL SH2 ... -

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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-KINASE
KeywordsTRANSFERASE/RECEPTOR / COMPLEX (PHOSPHOTRANSFERASE-RECEPTOR) / PHOSPHOTRANSFERASE / SH2 DOMAIN / SIGNAL TRANSDUCTION / PHOSPHOINOSITIDE 3-KINASE / TRANSFERASE-RECEPTOR complex
Function / homology
Function and homology information


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 / platelet activating factor receptor activity / 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-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 / platelet activating factor receptor activity / 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 / vascular endothelial growth factor binding / retina vasculature development in camera-type eye / 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 / IRS-mediated signalling / positive regulation of focal adhesion disassembly / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / myeloid leukocyte migration / Signaling by PDGF / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of chemotaxis / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / Activated NTRK3 signals through PI3K / cis-Golgi network / ErbB-3 class receptor binding / kinase activator activity / transmembrane receptor protein tyrosine kinase adaptor activity / platelet-derived growth factor receptor binding / RHOF GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of endoplasmic reticulum unfolded protein response / RHOD GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / enzyme-substrate adaptor activity / Nephrin family interactions / Signaling by LTK in cancer / Costimulation by the CD28 family / RND1 GTPase cycle / Signaling by LTK / MET activates PI3K/AKT signaling / positive regulation of leukocyte migration / PI3K/AKT activation / RND2 GTPase cycle / positive regulation of filopodium assembly / RND3 GTPase cycle / growth hormone receptor signaling pathway / negative regulation of stress fiber assembly / insulin binding / natural killer cell mediated cytotoxicity / RHOV GTPase cycle / negative regulation of cell-matrix adhesion / Signaling by ALK / positive regulation of DNA biosynthetic process / RHOB GTPase cycle / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR2 / positive regulation of calcium ion import / PI-3K cascade:FGFR4 / positive regulation of smooth muscle cell migration / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / negative regulation of osteoclast differentiation / platelet-derived growth factor receptor-beta signaling pathway / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / : / CD28 dependent PI3K/Akt signaling / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / CDC42 GTPase cycle / PI3K events in ERBB2 signaling / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / insulin receptor substrate binding / T cell differentiation / RHOG GTPase cycle / 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
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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Components

#1: Protein PHOSPHATIDYLINOSITOL 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


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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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