+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30535 | ||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of Schizosaccharomyces pombe Atg9 | ||||||||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||||||||
Sample |
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Keywords | Autophagy / membrane protein / UNKNOWN FUNCTION | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information Macroautophagy / : / phospholipid scramblase activity / protein localization to phagophore assembly site / phagophore assembly site membrane / autophagy of mitochondrion / fungal-type vacuole membrane / phagophore assembly site / autophagosome / macroautophagy ...Macroautophagy / : / phospholipid scramblase activity / protein localization to phagophore assembly site / phagophore assembly site membrane / autophagy of mitochondrion / fungal-type vacuole membrane / phagophore assembly site / autophagosome / macroautophagy / cytoplasmic vesicle membrane / autophagy / protein transport / membrane => GO:0016020 / Golgi membrane / endoplasmic reticulum membrane Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||||||||||||||||||||
Authors | Matoba K / Tsutsumi A | ||||||||||||||||||||||||||||||
Funding support | Japan, 9 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion. Authors: Kazuaki Matoba / Tetsuya Kotani / Akihisa Tsutsumi / Takuma Tsuji / Takaharu Mori / Daisuke Noshiro / Yuji Sugita / Norimichi Nomura / So Iwata / Yoshinori Ohsumi / Toyoshi Fujimoto / ...Authors: Kazuaki Matoba / Tetsuya Kotani / Akihisa Tsutsumi / Takuma Tsuji / Takaharu Mori / Daisuke Noshiro / Yuji Sugita / Norimichi Nomura / So Iwata / Yoshinori Ohsumi / Toyoshi Fujimoto / Hitoshi Nakatogawa / Masahide Kikkawa / Nobuo N Noda / Abstract: The molecular function of Atg9, the sole transmembrane protein in the autophagosome-forming machinery, remains unknown. Atg9 colocalizes with Atg2 at the expanding edge of the isolation membrane (IM) ...The molecular function of Atg9, the sole transmembrane protein in the autophagosome-forming machinery, remains unknown. Atg9 colocalizes with Atg2 at the expanding edge of the isolation membrane (IM), where Atg2 receives phospholipids from the endoplasmic reticulum (ER). Here we report that yeast and human Atg9 are lipid scramblases that translocate phospholipids between outer and inner leaflets of liposomes in vitro. Cryo-EM of fission yeast Atg9 reveals a homotrimer, with two connected pores forming a path between the two membrane leaflets: one pore, located at a protomer, opens laterally to the cytoplasmic leaflet; the other, at the trimer center, traverses the membrane vertically. Mutation of residues lining the pores impaired IM expansion and autophagy activity in yeast and abolished Atg9's ability to transport phospholipids between liposome leaflets. These results suggest that phospholipids delivered by Atg2 are translocated from the cytoplasmic to the luminal leaflet by Atg9, thereby driving autophagosomal membrane expansion. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30535.map.gz | 5.7 MB | EMDB map data format | |
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Header (meta data) | emd-30535-v30.xml emd-30535.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30535_fsc.xml | 7.8 KB | Display | FSC data file |
Images | emd_30535.png | 81.1 KB | ||
Masks | emd_30535_msk_1.map | 40.6 MB | Mask map | |
Filedesc metadata | emd-30535.cif.gz | 6.5 KB | ||
Others | emd_30535_half_map_1.map.gz emd_30535_half_map_2.map.gz | 31.2 MB 31.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30535 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30535 | HTTPS FTP |
-Related structure data
Related structure data | 7d0iMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30535.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_30535_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_30535_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_30535_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Protein detergent complex (Atg9-LMNG ) treated with GraFix
Entire | Name: Protein detergent complex (Atg9-LMNG ) treated with GraFix |
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Components |
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-Supramolecule #1: Protein detergent complex (Atg9-LMNG ) treated with GraFix
Supramolecule | Name: Protein detergent complex (Atg9-LMNG ) treated with GraFix type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) |
-Macromolecule #1: Autophagy-related protein 9
Macromolecule | Name: Autophagy-related protein 9 / type: protein_or_peptide / ID: 1 Details: A point mutation, S687Y, in the unobserved regions, is an unexpected mutation during plasmid preparation. C-terminal residues is linker (Gly-Ser) and cleaved site (Leu-Glu-Val-Leu-Phe-Gln). Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) |
Molecular weight | Theoretical: 82.742172 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MFYQPAQNKK QYDDLADIEA QNNVPNTQEV LEAWQESLDS DEDESSPLEE SNGFTISEHD DFVKSVPRKN NPTDLLYSGK LLDSDEPPS VHGNSSKVPS KHPSPSFPET TSLRNLQNGS KQKPALPNFN DPHFYNEDVT RSGHPNRSIY TQLPRNEFSN A RVLWNRLS ...String: MFYQPAQNKK QYDDLADIEA QNNVPNTQEV LEAWQESLDS DEDESSPLEE SNGFTISEHD DFVKSVPRKN NPTDLLYSGK LLDSDEPPS VHGNSSKVPS KHPSPSFPET TSLRNLQNGS KQKPALPNFN DPHFYNEDVT RSGHPNRSIY TQLPRNEFSN A RVLWNRLS ARDRVLWRWA NVENLDSFLQ QVYTYYTGKG LSCIIVHRLF QILTVSFVIG FTTFITSCID WPAVTPHGSL AG VTKSQCI AQMSPITYLV LWLFLSFLLA LWIYYLTDIP RLWQMREFYI HALKIATADM PTVSWQRVLY RLLKLKNVNA LTA EDGRVV SLHNMKRLDA YAIANRIMRK DNYFIALINN GIINIELPLL HRRILTHTTE WNINWCIFNF VFDEQGQLRS AFRN PNSRK RLSEELRRRF IVAGFLNCLF APIVAIYLVI HNFFRYFNEY HKNPGALSTR RYTPLALWTF REYNELQHFF DERIN DSYA AASHYVSQFP DFNMIRLFKY ISFILGSFTA ILVIITVFDP ELMVTFEITK DRSVLFYLGL FGSLIAVSRS IIPDET LVF APEKALRRVI TFTHYMPGWW SDNMHSKAVQ QEFCSLYSYR IVNLLWEILG ILLTPVLLFF TFPSCSQDIV DFFREHT IN VEGVGYVCSY AVFQDNPPYE SVASLVQSRK ISPLIQNKPE LSRIYFYEQF NTEAPRRDLR GSLEVLFQ UniProtKB: Autophagy-related protein 9 |
-Macromolecule #2: Lauryl Maltose Neopentyl Glycol
Macromolecule | Name: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 12 / Formula: LMN |
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Molecular weight | Theoretical: 1.005188 KDa |
Chemical component information | ChemComp-AV0: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||||||
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Buffer | pH: 8.3 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa / Details: The grid was washed by acetone prior to use | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |