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- PDB-8srm: Structure of human ULK1 complex core (2:2:2 stoichiometry) of the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8srm | |||||||||
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Title | Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant | |||||||||
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![]() | IMMUNE SYSTEM / Autophagy / Protein kinase / Complex | |||||||||
Function / homology | ![]() omegasome membrane / neuron projection regeneration / regulation of protein lipidation / ribophagy / negative regulation of collateral sprouting / glycophagy / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / positive regulation of autophagosome assembly / protein localization to phagophore assembly site ...omegasome membrane / neuron projection regeneration / regulation of protein lipidation / ribophagy / negative regulation of collateral sprouting / glycophagy / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / positive regulation of autophagosome assembly / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / protein kinase regulator activity / regulation of tumor necrosis factor-mediated signaling pathway / axon extension / phagophore assembly site / TBC/RABGAPs / reticulophagy / positive regulation of protein targeting to mitochondrion / Macroautophagy / Receptor Mediated Mitophagy / response to starvation / cellular response to nutrient levels / autophagosome membrane / mitophagy / positive regulation of cell size / autophagosome assembly / autophagosome / regulation of macroautophagy / negative regulation of protein-containing complex assembly / positive regulation of autophagy / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / protein serine/threonine kinase activator activity / liver development / negative regulation of extrinsic apoptotic signaling pathway / macroautophagy / Regulation of TNFR1 signaling / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / protein localization / recycling endosome / small GTPase binding / autophagy / neuron projection development / GTPase binding / heart development / peptidyl-serine phosphorylation / nuclear membrane / mitochondrial outer membrane / protein autophosphorylation / molecular adaptor activity / lysosome / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / cell cycle / negative regulation of cell population proliferation / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / signal transduction / mitochondrion / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.46 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 | ![]() | 183.4 KB | Display | ![]() |
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PDB format | ![]() | 119.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 55.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 40735MC ![]() 8soiC ![]() 8sorC ![]() 8sqzC ![]() 9c82C 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: 73325.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 24190.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: O75385, non-specific serine/threonine protein kinase #3: Protein | Mass: 8150.997 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-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: Human autophagy initiation ULK1 complex core / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.21 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.35 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 |
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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: ![]() |
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: 2286 |
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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: 968884 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148675 / 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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