+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22375 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of human ATG9A in amphipols | |||||||||
Map data | primary map | |||||||||
Sample |
| |||||||||
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 / bone morphogenesis / phagophore assembly site / autophagy of mitochondrion / reticulophagy / Macroautophagy ...phospholipid scramblase activity / programmed necrotic cell death / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / bone morphogenesis / phagophore assembly site / autophagy of mitochondrion / reticulophagy / Macroautophagy / autophagosome assembly / autophagosome / PINK1-PRKN Mediated Mitophagy / mitochondrial membrane / trans-Golgi network / 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 | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Maeda S / Otomo T | |||||||||
Funding support | United States, 1 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22375.map.gz | 25 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-22375-v30.xml emd-22375.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22375_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_22375.png | 55.7 KB | ||
Others | emd_22375_additional_1.map.gz emd_22375_half_map_1.map.gz emd_22375_half_map_2.map.gz | 20.6 MB 20.6 MB 20.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22375 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22375 | HTTPS FTP |
-Validation report
Summary document | emd_22375_validation.pdf.gz | 748.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_22375_full_validation.pdf.gz | 748.3 KB | Display | |
Data in XML | emd_22375_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | emd_22375_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22375 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22375 | HTTPS FTP |
-Related structure data
Related structure data | 7jloMC 7jlpC 7jlqC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_22375.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.134 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: raw map
File | emd_22375_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | raw map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 1
File | emd_22375_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 2
File | emd_22375_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Human ATG9A in amphipols A8-35
Entire | Name: Human ATG9A in amphipols A8-35 |
---|---|
Components |
|
-Supramolecule #1: Human ATG9A in amphipols A8-35
Supramolecule | Name: Human ATG9A in amphipols A8-35 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Autophagy-related protein 9A
Macromolecule | Name: Autophagy-related protein 9A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 66.797344 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAQFDTEYQR LEASYSDSPP GEEDLLVHVA EGSKSPWHHI ENLDLFFSRV YNLHQKNGFT CMLIGEIFEL MQFLFVVAFT TFLVSCVDY DILFANKMVN HSLHPTEPVK VTLPDAFLPA QVCSARIQEN GSLITILVIA GVFWIHRLIK FIYNICCYWE I HSFYLHAL ...String: MAQFDTEYQR LEASYSDSPP GEEDLLVHVA EGSKSPWHHI ENLDLFFSRV YNLHQKNGFT CMLIGEIFEL MQFLFVVAFT TFLVSCVDY DILFANKMVN HSLHPTEPVK VTLPDAFLPA QVCSARIQEN GSLITILVIA GVFWIHRLIK FIYNICCYWE I HSFYLHAL RIPMSALPYC TWQEVQARIV QTQKEHQICI HKRELTELDI YHRILRFQNY MVALVNKSLL PLRFRLPGLG EA VFFTRGL KYNFELILFW GPGSLFLNEW SLKAEYKRGG QRLELAQRLS NRILWIGIAN FLLCPLILIW QILYAFFSYA EVL KREPGA LGARCWSLYG RCYLRHFNEL EHELQSRLNR GYKPASKYMN CFLSPLLTLL AKNGAFFAGS ILAVLIALTI YDED VLAVE HVLTTVTLLG VTVTVCRSFI PDQHMVFCPE QLLRVILAHI HYMPDHWQGN AHRSQTRDEF AQLFQYKAVF ILEEL LSPI VTPLILIFCL RPRALEIIDF FRNFTVEVVG VGDTCSFAQM DVRQHGHPQW LSAGQTEASV YQQAEDGKTE LSLMHF AIT NPGWQPPRES TAFLG |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 12 mg/mL |
---|---|
Buffer | pH: 7.5 |
Grid | Model: UltrAuFoil R1.2/1.3 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 88 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 73000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |