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- PDB-5gji: PI3K p85 N-terminal SH2 domain/CD28-derived peptide complex -

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Basic information

Entry
Database: PDB / ID: 5gji
TitlePI3K p85 N-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 / kinase activator activity / RHOF GTPase cycle / 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 / Role of phospholipids in phagocytosis / GAB1 signalosome / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of viral genome replication / 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: 0.9 Å
AuthorsInaba, S. / Numoto, N. / Morii, H. / Ogawa, S. / Ikura, T. / Abe, R. / Ito, N. / Oda, M.
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
DepositionJun 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references

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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)13,8516
Polymers13,4712
Non-polymers3804
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-46 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.590, 31.240, 32.250
Angle α, β, γ (deg.)73.28, 85.38, 71.73
Int Tables number1
Space group name H-MP1

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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: 12432.955 Da / Num. of mol.: 1 / Fragment: UNP residues 325-430 / Mutation: D330N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Plasmid: pGEX-4T-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM Sodium acetate trihydrate, 30% PEG MME 2000, 200mM Ammonium sulfate

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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: May 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 0.9→30.9 Å / Num. obs: 65076 / % possible obs: 89.5 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.1
Reflection shellResolution: 0.9→0.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4 / CC1/2: 0.92 / % possible all: 81.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSMarch 1, 2015data reduction
XSCALEMarch 1, 2015data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.9→30.884 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 12.05
RfactorNum. reflection% reflection
Rfree0.1446 3260 5.01 %
Rwork0.1259 --
obs0.1268 65076 89.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.9→30.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 21 190 1153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071120
X-RAY DIFFRACTIONf_angle_d1.3871534
X-RAY DIFFRACTIONf_dihedral_angle_d12.605435
X-RAY DIFFRACTIONf_chiral_restr0.058157
X-RAY DIFFRACTIONf_plane_restr0.007200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9003-0.91380.23321220.23872229X-RAY DIFFRACTION75
0.9138-0.92810.21431290.19352535X-RAY DIFFRACTION85
0.9281-0.94330.18691360.15692551X-RAY DIFFRACTION84
0.9433-0.95950.14081150.13662568X-RAY DIFFRACTION86
0.9595-0.9770.1511370.12842564X-RAY DIFFRACTION85
0.977-0.99580.1561410.1222583X-RAY DIFFRACTION87
0.9958-1.01610.13181400.11042606X-RAY DIFFRACTION87
1.0161-1.03820.1091480.10512581X-RAY DIFFRACTION87
1.0382-1.06240.11591560.0972629X-RAY DIFFRACTION88
1.0624-1.08890.1041460.09472616X-RAY DIFFRACTION88
1.0889-1.11840.1131520.09232691X-RAY DIFFRACTION89
1.1184-1.15130.10131500.08842713X-RAY DIFFRACTION90
1.1513-1.18840.11071510.08892658X-RAY DIFFRACTION90
1.1884-1.23090.10631270.09222749X-RAY DIFFRACTION91
1.2309-1.28020.10821270.09732756X-RAY DIFFRACTION92
1.2802-1.33850.11331390.10332772X-RAY DIFFRACTION92
1.3385-1.4090.11951430.10452800X-RAY DIFFRACTION93
1.409-1.49730.10821590.10652798X-RAY DIFFRACTION94
1.4973-1.61290.13691420.11342825X-RAY DIFFRACTION95
1.6129-1.77520.13431320.132865X-RAY DIFFRACTION95
1.7752-2.0320.15061500.14132904X-RAY DIFFRACTION96
2.032-2.560.17231530.14642913X-RAY DIFFRACTION97
2.56-30.90230.18981650.15222910X-RAY DIFFRACTION97

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