+Open data
-Basic information
Entry | Database: PDB / ID: 7jlq | ||||||
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Title | cryo-EM structure of human ATG9A in LMNG micelles | ||||||
Components | Autophagy-related protein 9A | ||||||
Keywords | MEMBRANE PROTEIN / autophagy | ||||||
Function / homology | Function and homology information phospholipid scramblase activity / programmed necrotic cell death / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / bone morphogenesis / reticulophagy / Macroautophagy / autophagosome assembly ...phospholipid scramblase activity / programmed necrotic cell death / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / bone morphogenesis / reticulophagy / Macroautophagy / autophagosome assembly / autophagosome / trans-Golgi network / mitochondrial membrane / recycling endosome / recycling endosome membrane / late endosome / late endosome membrane / endosome / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Maeda, S. / Otomo, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. Authors: Shintaro Maeda / Hayashi Yamamoto / Lisa N Kinch / Christina M Garza / Satoru Takahashi / Chinatsu Otomo / Nick V Grishin / Stefano Forli / Noboru Mizushima / Takanori Otomo / Abstract: De novo formation of the double-membrane compartment autophagosome is seeded by small vesicles carrying membrane protein autophagy-related 9 (ATG9), the function of which remains unknown. Here we ...De novo formation of the double-membrane compartment autophagosome is seeded by small vesicles carrying membrane protein autophagy-related 9 (ATG9), the function of which remains unknown. Here we find that ATG9A scrambles phospholipids of membranes in vitro. Cryo-EM structures of human ATG9A reveal a trimer with a solvated central pore, which is connected laterally to the cytosol through the cavity within each protomer. Similarities to ABC exporters suggest that ATG9A could be a transporter that uses the central pore to function. Moreover, molecular dynamics simulation suggests that the central pore opens laterally to accommodate lipid headgroups, thereby enabling lipids to flip. Mutations in the pore reduce scrambling activity and yield markedly smaller autophagosomes, indicating that lipid scrambling by ATG9A is essential for membrane expansion. We propose ATG9A acts as a membrane-embedded funnel to facilitate lipid flipping and to redistribute lipids added to the outer leaflet of ATG9 vesicles, thereby enabling growth into autophagosomes. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7jlq.cif.gz | 264 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jlq.ent.gz | 215.6 KB | Display | PDB format |
PDBx/mmJSON format | 7jlq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jlq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7jlq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7jlq_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 7jlq_validation.cif.gz | 75.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/7jlq ftp://data.pdbj.org/pub/pdb/validation_reports/jl/7jlq | HTTPS FTP |
-Related structure data
Related structure data | 22377MC 7jloC 7jlpC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 66797.344 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATG9A, APG9L1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7Z3C6 |
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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 ATG9A in LMNG micelles / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 88 % / 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: 73000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 66 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40116 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7JLP | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 126.57 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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