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Yorodumi- PDB-8sqz: Structure of human ULK1 complex core (2:2:2 stoichiometry) in the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sqz | |||||||||
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Title | Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Autophagy / Protein kinase / Complex | |||||||||
Function / homology | Function and homology information omegasome membrane / neuron projection regeneration / regulation of protein lipidation / ribophagy / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / autophagy of peroxisome / glycophagy / response to mitochondrial depolarisation / positive regulation of autophagosome assembly ...omegasome membrane / neuron projection regeneration / regulation of protein lipidation / ribophagy / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / autophagy of peroxisome / glycophagy / 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 / regulation of tumor necrosis factor-mediated signaling pathway / protein kinase regulator activity / axon extension / TBC/RABGAPs / phagophore assembly site / autophagy of mitochondrion / reticulophagy / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Macroautophagy / response to starvation / autophagosome membrane / positive regulation of cell size / autophagosome assembly / mitophagy / regulation of macroautophagy / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / positive regulation of autophagy / protein-membrane adaptor activity / extrinsic apoptotic signaling pathway / autophagosome / protein serine/threonine kinase activator activity / liver development / negative regulation of extrinsic apoptotic signaling pathway / peptidyl-threonine phosphorylation / macroautophagy / Regulation of TNFR1 signaling / positive regulation of JNK cascade / recycling endosome / small GTPase binding / autophagy / neuron projection development / protein localization / 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 / protein phosphorylation / negative regulation of cell population proliferation / axon / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex binding / protein kinase binding / signal transduction / mitochondrion / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.85 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 | 8sqz.cif.gz | 226.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sqz.ent.gz | 152.5 KB | Display | PDB format |
PDBx/mmJSON format | 8sqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sqz_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8sqz_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8sqz_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 8sqz_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/8sqz ftp://data.pdbj.org/pub/pdb/validation_reports/sq/8sqz | HTTPS FTP |
-Related structure data
Related structure data | 40715MC 8soiC 8sorC 8srmC 9c82C 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: 73325.633 Da / Num. of mol.: 2 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 #2: Protein | Mass: 24190.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722 / Production host: Homo sapiens (human) References: UniProt: O75385, non-specific serine/threonine protein kinase #3: Protein | Mass: 17096.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATG13, KIAA0652 / Production host: Homo sapiens (human) / References: UniProt: O75143 |
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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 |
-Sample preparation
Component | Name: Human autophagy initiation ULK1 complex core / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.23 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 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 R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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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 / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
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: 5383 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 97987 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97987 / 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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