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- PDB-7cio: Molecular interactions of cytoplasmic region of CTLA-4 with SH2 d... -

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Basic information

Entry
Database: PDB / ID: 7cio
TitleMolecular interactions of cytoplasmic region of CTLA-4 with SH2 domains of PI3-kinase
Components
  • Cytotoxic T-lymphocyte protein 4
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
KeywordsSIGNALING PROTEIN / T-CELL / CD28 / PHOSPHOPEPTIDES / PROTEIN ENGINEERING / THERMOSTABILITY
Function / homology
Function and homology information


protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / perinuclear endoplasmic reticulum membrane / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / clathrin-coated endocytic vesicle / positive regulation of focal adhesion disassembly / IRS-mediated signalling ...protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / perinuclear endoplasmic reticulum membrane / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / regulation of toll-like receptor 4 signaling pathway / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / clathrin-coated endocytic vesicle / 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 / 1-phosphatidylinositol-3-kinase regulator activity / 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 / 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 / CTLA4 inhibitory signaling / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR2 / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / RHOC GTPase cycle / negative regulation of B cell proliferation / 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 / CDC42 GTPase cycle / RHOU GTPase cycle / PI3K events in ERBB2 signaling / 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 / Interleukin receptor SHC signaling / 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 / negative 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 / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / Interleukin-7 signaling / phosphotyrosine residue binding / response to endoplasmic reticulum stress / Downstream signal transduction / B cell differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / substrate adhesion-dependent cell spreading
Similarity search - Function
Cytotoxic T-lymphocyte antigen 4 / 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 ...Cytotoxic T-lymphocyte antigen 4 / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / 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 subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Cytotoxic T-lymphocyte protein 4 / Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsIiyama, M. / Numoto, N. / Ogawa, S. / Kuroda, M. / Morii, H. / Abe, R. / Ito, N. / Oda, M.
CitationJournal: Mol.Immunol. / Year: 2021
Title: Molecular interactions of the CTLA-4 cytoplasmic region with the phosphoinositide 3-kinase SH2 domains.
Authors: Iiyama, M. / Numoto, N. / Ogawa, S. / Kuroda, M. / Morii, H. / Abe, R. / Ito, N. / Oda, M.
History
DepositionJul 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Nov 29, 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

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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: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)13,1502
Polymers13,1502
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area6160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.221, 41.563, 59.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 12178.474 Da / Num. of mol.: 1 / Mutation: C656S, C659V, C670L
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) / References: UniProt: P27986
#2: Protein/peptide Cytotoxic T-lymphocyte protein 4 / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 971.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P16410
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate pH 4.6, 30% PEG 4000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 18, 2019
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: 40740 / % possible obs: 96.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 12.24 Å2 / CC1/2: 0.999 / Rsym value: 0.062 / Net I/σ(I): 15.4
Reflection shellResolution: 1.1→1.17 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5178 / CC1/2: 0.689 / Rsym value: 0.884 / % possible all: 77.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AUL

5aul


Resolution: 1.1→34.1 Å / SU ML: 0.113 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.8847 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1787 2037 5 %
Rwork0.1537 38688 -
obs0.1549 40725 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.78 Å2
Refinement stepCycle: LAST / Resolution: 1.1→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 0 169 1096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123984
X-RAY DIFFRACTIONf_angle_d1.31181346
X-RAY DIFFRACTIONf_chiral_restr0.1075148
X-RAY DIFFRACTIONf_plane_restr0.0097173
X-RAY DIFFRACTIONf_dihedral_angle_d11.832365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.130.2568870.241749X-RAY DIFFRACTION65.97
1.13-1.150.25371140.22272128X-RAY DIFFRACTION80.85
1.15-1.180.21861400.2022568X-RAY DIFFRACTION97.69
1.18-1.220.26181260.19542651X-RAY DIFFRACTION99.96
1.22-1.260.24121500.19832630X-RAY DIFFRACTION99.96
1.26-1.30.23081610.19262636X-RAY DIFFRACTION99.93
1.3-1.360.2291420.1812645X-RAY DIFFRACTION99.93
1.36-1.420.17351350.16362664X-RAY DIFFRACTION99.82
1.42-1.490.16451280.14952692X-RAY DIFFRACTION99.89
1.49-1.590.16871450.12982646X-RAY DIFFRACTION99.86
1.59-1.710.17971410.12242674X-RAY DIFFRACTION99.93
1.71-1.880.17221560.13932676X-RAY DIFFRACTION99.82
1.88-2.150.15831220.13672731X-RAY DIFFRACTION99.96
2.15-2.710.18711390.15432732X-RAY DIFFRACTION99.76
2.71-34.10.1571510.1512866X-RAY DIFFRACTION99.67

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