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Open data
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Basic information
Entry | Database: PDB / ID: 9c82 | |||||||||
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Title | Structure of human ULK1C:PI3KC3-C1 supercomplex | |||||||||
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![]() | IMMUNE SYSTEM / Autophagy / Protein kinase / Lipid kinase / Supercomplex | |||||||||
Function / homology | ![]() 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 / regulation of protein lipidation / Synthesis of PIPs at the late endosome membrane ...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 / regulation of protein lipidation / Synthesis of PIPs at the late endosome membrane / ribophagy / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / glycophagy / Atg1/ULK1 kinase complex / mitochondria-associated endoplasmic reticulum membrane contact site / 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 / positive regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / regulation of protein complex stability / engulfment of apoptotic cell / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / phagophore assembly site membrane / suppression by virus of host autophagy / protein targeting to lysosome / protein targeting to vacuole / early endosome to late endosome transport / late endosome to vacuole transport / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / SMAD protein signal transduction / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / negative regulation of programmed cell death / response to iron(II) ion / reticulophagy / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / post-transcriptional regulation of gene expression / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / Macroautophagy / 1-phosphatidylinositol-3-kinase activity / autophagosome membrane docking / RSV-host interactions / lysosome organization / endosome to lysosome transport / positive regulation of cardiac muscle hypertrophy / p38MAPK cascade / axoneme / phosphatidylinositol-mediated signaling / autophagosome membrane / phosphatidylinositol phosphate biosynthetic process / mitophagy / autophagosome maturation / positive regulation of cell size / autophagosome assembly / PI3K Cascade / RHO GTPases Activate NADPH Oxidases / negative regulation of reactive oxygen species metabolic process / neuron development / autophagosome / response to vitamin E / regulation of macroautophagy / amyloid-beta metabolic process / cellular defense response / cellular response to glucose starvation / positive regulation of autophagy / phosphatidylinositol 3-kinase binding / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / JNK cascade / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / phagocytic vesicle / cellular response to starvation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of protein phosphorylation / regulation of cytokinesis / liver development / regulation of autophagy / negative regulation of extrinsic apoptotic signaling pathway / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of JNK cascade / response to lead ion Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.84 Å | |||||||||
![]() | Chen, M. / Hurley, J.H. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 75 KB | Display | |
Data in CIF | ![]() | 115 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 40738MC ![]() 45297MC ![]() 8soiC ![]() 8sorC ![]() 8sqzC ![]() 8srmC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 153293.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q99570, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 101680.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 55387.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 51953.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Protein | Mass: 73325.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Supercomplex composed of ULK1 complex and PI3KC3-C1 complex Type: COMPLEX Details: Individually expressed the ULK1 complex core (consists of two molecules of FIP200 (1-640), ULK1 (828-1050), and ATG13 (363-517)) and the full-length PI3KC3-C1 (consists of VPS34, VPS15, ...Details: Individually expressed the ULK1 complex core (consists of two molecules of FIP200 (1-640), ULK1 (828-1050), and ATG13 (363-517)) and the full-length PI3KC3-C1 (consists of VPS34, VPS15, BECN1, and ATG14). Mixed the above two complexes in a molecular ratio of 1.5:1 and purified the supercomplex by strep pulldown of the TSF-tagged VPS15. Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight |
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Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was purified by strep pulldown. | ||||||||||||||||||||||||||||||
Specimen support | Details: 25 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: added 0.05% (w/v) octylglucopyranoside as surfactant |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4473551 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21937 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |