+Open data
-Basic information
Entry | Database: PDB / ID: 8aj8 | |||||||||
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Title | Structure of p110 gamma bound to the p84 regulatory subunit | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / PI3K / PIK3CG / PIK3R6 / phosphoinositide 3-kinase / p110 / p84 | |||||||||
Function / homology | Function and homology information G beta:gamma signalling through PI3Kgamma / GPVI-mediated activation cascade / regulation of natural killer cell mediated cytotoxicity / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-4-phosphate 3-kinase / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity ...G beta:gamma signalling through PI3Kgamma / GPVI-mediated activation cascade / regulation of natural killer cell mediated cytotoxicity / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-4-phosphate 3-kinase / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / positive regulation of T cell differentiation / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / immune system process / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAP kinase activity / endocytosis / positive regulation of angiogenesis / chemotaxis / angiogenesis / non-specific serine/threonine protein kinase / inflammatory response / G protein-coupled receptor signaling pathway / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8.5 Å | |||||||||
Authors | Burke, J.E. / Williams, R.L. / Zhang, X. | |||||||||
Funding support | United Kingdom, Canada, 2items
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Citation | Journal: Cell Rep / Year: 2023 Title: Molecular basis for differential activation of p101 and p84 complexes of PI3Kγ by Ras and GPCRs. Authors: Manoj K Rathinaswamy / Meredith L Jenkins / Benjamin R Duewell / Xuxiao Zhang / Noah J Harris / John T Evans / Jordan T B Stariha / Udit Dalwadi / Kaelin D Fleming / Harish Ranga-Prasad / ...Authors: Manoj K Rathinaswamy / Meredith L Jenkins / Benjamin R Duewell / Xuxiao Zhang / Noah J Harris / John T Evans / Jordan T B Stariha / Udit Dalwadi / Kaelin D Fleming / Harish Ranga-Prasad / Calvin K Yip / Roger L Williams / Scott D Hansen / John E Burke / Abstract: Class IB phosphoinositide 3-kinase (PI3Kγ) is activated in immune cells and can form two distinct complexes (p110γ-p84 and p110γ-p101), which are differentially activated by G protein-coupled ...Class IB phosphoinositide 3-kinase (PI3Kγ) is activated in immune cells and can form two distinct complexes (p110γ-p84 and p110γ-p101), which are differentially activated by G protein-coupled receptors (GPCRs) and Ras. Using a combination of X-ray crystallography, hydrogen deuterium exchange mass spectrometry (HDX-MS), electron microscopy, molecular modeling, single-molecule imaging, and activity assays, we identify molecular differences between p110γ-p84 and p110γ-p101 that explain their differential membrane recruitment and activation by Ras and GPCRs. The p110γ-p84 complex is dynamic compared with p110γ-p101. While p110γ-p101 is robustly recruited by Gβγ subunits, p110γ-p84 is weakly recruited to membranes by Gβγ subunits alone and requires recruitment by Ras to allow for Gβγ activation. We mapped two distinct Gβγ interfaces on p101 and the p110γ helical domain, with differences in the C-terminal domain of p84 and p101 conferring sensitivity of p110γ-p101 to Gβγ activation. Overall, our work provides key insight into the molecular basis for how PI3Kγ complexes are activated. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aj8.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8aj8.ent.gz | 2.1 MB | Display | PDB format |
PDBx/mmJSON format | 8aj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/8aj8 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/8aj8 | HTTPS FTP |
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-Related structure data
Related structure data | 7mezS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 126830.812 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: PIK3CG / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O02697, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, phosphatidylinositol-4-phosphate 3-kinase, non-specific serine/threonine protein kinase #2: Protein | Mass: 84769.906 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pik3r6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3U6Q4 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.81 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: Optimized crystals were grown from a crystallization solution containing 16% EDO_P8K (20% w/v PEG 8000, 40% v/v ethylene glycol), 0.06 M amino acids (0.2 M sodium L-glutamate, 0.2 M DL- ...Details: Optimized crystals were grown from a crystallization solution containing 16% EDO_P8K (20% w/v PEG 8000, 40% v/v ethylene glycol), 0.06 M amino acids (0.2 M sodium L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine, 0.2 M DL-serine), 0.08 M buffer 2 pH7.5 (0.5 M HEPES, 0.5 M MOPS), 0.4 M Na/K phosphate pH 6.3. PH range: 6.3-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 8.5→90.3 Å / Num. obs: 10835 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 484.61 Å2 / CC1/2: 0.99 / CC star: 0.129 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.066 / Rrim(I) all: 0.129 / Rsym value: 0.122 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 8.5→8.89 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1187 / CC1/2: 0.9 / Rpim(I) all: 0.228 / Rrim(I) all: 0.463 / Rsym value: 0.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7MEZ Resolution: 8.5→90.29 Å / SU ML: 1.2545 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.6969 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 545.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 8.5→90.29 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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