+Open data
-Basic information
Entry | Database: PDB / ID: 9c82 | |||||||||
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Title | Structure of human ULK1C:PI3KC3-C1 supercomplex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Autophagy / Protein kinase / Lipid kinase / Supercomplex | |||||||||
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 / regulation of protein lipidation ...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 / regulation of protein lipidation / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / ribophagy / 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 / Atg1/ULK1 kinase complex / mitochondria-associated endoplasmic reticulum membrane contact site / autophagy of peroxisome / glycophagy / 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 / piecemeal microautophagy of the nucleus / 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 / autophagy of mitochondrion / response to iron(II) ion / cellular response to nitrogen starvation / reticulophagy / 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 / positive regulation of cell size / 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 / extrinsic apoptotic signaling pathway / 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 / liver development / regulation of cytokinesis / regulation of autophagy / negative regulation of extrinsic apoptotic signaling pathway / macroautophagy Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.84 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 | 9c82.cif.gz | 359 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9c82.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9c82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9c82_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 9c82_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 9c82_validation.xml.gz | 75 KB | Display | |
Data in CIF | 9c82_validation.cif.gz | 115 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/9c82 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/9c82 | HTTPS FTP |
-Related structure data
Related structure data | 40738MC 45297MC 8soiC 8sorC 8sqzC 8srmC C: citing same article (ref.) M: map data used to model this data |
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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: 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 |
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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.) Homo sapiens (human) / Gene: PIK3C3, VPS34 / Production host: Homo sapiens (human) / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase |
#3: 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 |
#4: 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 |
#5: Protein | Mass: 73325.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RB1CC1, KIAA0203, RBICC / Production host: Homo sapiens (human) / References: UniProt: Q8TDY2 |
-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: 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: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
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 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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 |