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- PDB-5aul: PI3K p85 C-terminal SH2 domain/CD28-derived peptide complex -

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Basic information

Entry
Database: PDB / ID: 5aul
TitlePI3K p85 C-terminal SH2 domain/CD28-derived peptide complex
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • T-cell-specific surface glycoprotein CD28
KeywordsSIGNALING PROTEIN / Antigens / Phosphopeptides
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / regulatory T cell differentiation / positive regulation of inflammatory response to antigenic stimulus / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection ...Nef mediated downregulation of CD28 cell surface expression / regulatory T cell differentiation / positive regulation of inflammatory response to antigenic stimulus / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / IRS-mediated signalling / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / myeloid leukocyte migration / positive regulation of CD4-positive, alpha-beta T cell proliferation / 1-phosphatidylinositol-3-kinase regulator activity / CD28 co-stimulation / 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 / RHOF GTPase cycle / kinase activator activity / transmembrane receptor protein tyrosine kinase adaptor activity / RHOD GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / CD28 dependent Vav1 pathway / positive regulation of leukocyte migration / MET activates PI3K/AKT signaling / RND2 GTPase cycle / PI3K/AKT activation / positive regulation of filopodium assembly / RND3 GTPase cycle / negative regulation of stress fiber assembly / growth hormone receptor signaling pathway / insulin binding / RHOV GTPase cycle / negative regulation of cell-matrix adhesion / Signaling by ALK / RHOB GTPase cycle / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / positive regulation of interleukin-4 production / PI-3K cascade:FGFR2 / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / RHOC GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / positive regulation of interleukin-10 production / CDC42 GTPase cycle / RHOU GTPase cycle / humoral immune response / PI3K events in ERBB2 signaling / immunological synapse / T cell differentiation / RET signaling / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / RHOG GTPase cycle / extrinsic apoptotic signaling pathway via death domain receptors / PI3K Cascade / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of viral genome replication / Role of phospholipids in phagocytosis / GAB1 signalosome / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / coreceptor activity / phosphatidylinositol 3-kinase binding / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / positive regulation of lamellipodium assembly / Signaling by FGFR4 in disease / positive regulation of T cell proliferation / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR3 in disease / Tie2 Signaling / GPVI-mediated activation cascade / Signaling by FGFR2 in disease
Similarity search - Function
T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / 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 ...T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / 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 / Immunoglobulin V-Type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Immunoglobulin V-set domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
T-cell-specific surface glycoprotein CD28 / Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsInaba, S. / Numoto, N. / Morii, H. / Ikura, T. / Oda, M. / Ito, N.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins
Authors: Inaba, S. / Numoto, N. / Ogawa, S. / Morii, H. / Ikura, T. / Abe, R. / Ito, N. / Oda, M.
History
DepositionApr 28, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Nov 8, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 3-kinase regulatory subunit alpha
B: T-cell-specific surface glycoprotein CD28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3353
Polymers13,2432
Non-polymers921
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-12 kcal/mol
Surface area6110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.600, 41.440, 64.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylinositol 3-kinase regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit ...PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PtdIns-3-kinase regulatory subunit p85-alpha


Mass: 12204.536 Da / Num. of mol.: 1 / Fragment: UNP residues 614-720
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P27986
#2: Protein/peptide T-cell-specific surface glycoprotein CD28 / TP44


Mass: 1038.047 Da / Num. of mol.: 1 / Fragment: UNP residues 189-196 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10747
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Sodium Acetate trihydrate, 200 mM Ammonium Acetate, 30% PEG4000
PH range: 4.6

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 45133 / % possible obs: 100 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.7
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
REFMACrefinement
PHASERphasing
XDSdata processing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H9O

1h9o


Resolution: 1.1→34.919 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1603 2248 4.98 %
Rwork0.1376 --
obs0.1387 45133 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→34.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 6 181 1101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171139
X-RAY DIFFRACTIONf_angle_d1.9031552
X-RAY DIFFRACTIONf_dihedral_angle_d18.14435
X-RAY DIFFRACTIONf_chiral_restr0.117163
X-RAY DIFFRACTIONf_plane_restr0.011204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1001-1.1240.16581510.15122614X-RAY DIFFRACTION100
1.124-1.15010.15871320.14142627X-RAY DIFFRACTION100
1.1501-1.17890.14421250.13452674X-RAY DIFFRACTION100
1.1789-1.21080.18571300.13272662X-RAY DIFFRACTION100
1.2108-1.24640.16461390.13762634X-RAY DIFFRACTION100
1.2464-1.28660.18381490.12982645X-RAY DIFFRACTION100
1.2866-1.33260.14891560.12522636X-RAY DIFFRACTION100
1.3326-1.3860.14511540.11472635X-RAY DIFFRACTION100
1.386-1.4490.15751390.11682699X-RAY DIFFRACTION100
1.449-1.52540.15011150.11122670X-RAY DIFFRACTION100
1.5254-1.6210.1571500.11372673X-RAY DIFFRACTION100
1.621-1.74620.14661390.12142677X-RAY DIFFRACTION100
1.7462-1.92190.14841560.12782693X-RAY DIFFRACTION100
1.9219-2.19990.17191260.13362715X-RAY DIFFRACTION100
2.1999-2.77150.16971360.15752756X-RAY DIFFRACTION100
2.7715-34.9370.16021510.15532875X-RAY DIFFRACTION100

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