+Open data
-Basic information
Entry | Database: PDB / ID: 8sor | |||||||||
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Title | Structure of human PI3KC3-C1 complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Autophagy / Lipid kinase / Complex | |||||||||
Function / homology | Function and homology information extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / nucleus-vacuole junction / cellular response to aluminum ion / Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III ...extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / extrinsic component of phagophore assembly site membrane / nucleus-vacuole junction / cellular response to aluminum ion / Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of stress granule assembly / mitochondria-associated endoplasmic reticulum membrane contact site / autophagy of peroxisome / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / positive regulation by host of viral genome replication / Synthesis of PIPs at the Golgi membrane / receptor catabolic process / positive regulation of autophagosome assembly / engulfment of apoptotic cell / phosphatidylinositol kinase activity / negative regulation of autophagosome assembly / regulation of protein complex stability / phosphatidylinositol 3-kinase regulator activity / protein targeting to vacuole / suppression by virus of host autophagy / protein localization to phagophore assembly site / protein targeting to lysosome / phagophore assembly site membrane / late endosome to vacuole transport / early endosome to late endosome transport / SMAD protein signal transduction / negative regulation of programmed cell death / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / cytoplasmic pattern recognition receptor signaling pathway / response to iron(II) ion / cellular response to nitrogen starvation / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / autophagosome membrane docking / mitotic metaphase chromosome alignment / post-transcriptional regulation of gene expression / 1-phosphatidylinositol-3-kinase activity / endosome to lysosome transport / lysosome organization / Macroautophagy / RSV-host interactions / positive regulation of cardiac muscle hypertrophy / autolysosome / p38MAPK cascade / phosphatidylinositol-mediated signaling / axoneme / phosphatidylinositol phosphate biosynthetic process / autophagosome membrane / PI3K Cascade / autophagosome maturation / neuron development / autophagosome assembly / mitophagy / RHO GTPases Activate NADPH Oxidases / response to vitamin E / negative regulation of reactive oxygen species metabolic process / amyloid-beta metabolic process / regulation of macroautophagy / cellular defense response / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / phagocytic vesicle / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of autophagy / protein-membrane adaptor activity / JNK cascade / cellular response to copper ion / cellular response to epidermal growth factor stimulus / cellular response to amino acid starvation / autophagosome / cellular response to starvation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of protein phosphorylation / regulation of cytokinesis / regulation of autophagy / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to lead ion / regulation of protein phosphorylation / trans-Golgi network / ISG15 antiviral mechanism / autophagy / cellular response to hydrogen peroxide / endocytosis / phagocytic vesicle membrane / microtubule cytoskeleton / late endosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 Å | |||||||||
Authors | Chen, M. / Hurley, J.H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: bioRxiv / Year: 2023 Title: Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex Authors: Chen, M. / Ren, X. / Cook, A. / Hurley, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sor.cif.gz | 695.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sor.ent.gz | 559 KB | Display | PDB format |
PDBx/mmJSON format | 8sor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sor_validation.pdf.gz | 909.3 KB | Display | wwPDB validaton report |
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Full document | 8sor_full_validation.pdf.gz | 929.7 KB | Display | |
Data in XML | 8sor_validation.xml.gz | 55.1 KB | Display | |
Data in CIF | 8sor_validation.cif.gz | 84 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/8sor ftp://data.pdbj.org/pub/pdb/validation_reports/so/8sor | HTTPS FTP |
-Related structure data
Related structure data | 40669MC 8soiC 8sqzC 8srmC 9c82C M: map data used to model this data 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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1 |
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-Components
#1: Protein | Mass: 101680.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3, VPS34 / Production host: Homo sapiens (human) / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase |
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#2: Protein | Mass: 55387.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATG14 / Production host: Homo sapiens (human) / References: UniProt: Q6ZNE5 |
#3: Protein | Mass: 51953.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BECN1, GT197 / Production host: Homo sapiens (human) / References: UniProt: Q14457 |
#4: Protein | Mass: 153293.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R4, VPS15 / Production host: Homo sapiens (human) References: UniProt: Q99570, non-specific serine/threonine protein kinase |
#5: Chemical | ChemComp-ADP / |
Has ligand of interest | Y |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human autophagy initiation PI3KC3-C1 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.362 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK GnTi- | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: 25 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2243 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1229932 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266147 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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