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- EMDB-17789: Structure of tissue-specific lipid scramblase ATG9B homotrimer, r... -
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Open data
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Basic information
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Title | Structure of tissue-specific lipid scramblase ATG9B homotrimer, refined with C3 symmetry applied | ||||||||||||||||||
![]() | ATG9B C3 map | ||||||||||||||||||
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![]() | membrane protein / lipid scramblase / autophagy / phagopore / lipid transporter / Atg9 / Atg9B / LIPID TRANSPORT | ||||||||||||||||||
Function / homology | ![]() 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 / recycling endosome membrane / Golgi membrane / endoplasmic reticulum membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||||||||
![]() | Chiduza GN / Pye VE / Tooze SA / Cherepanov P | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A. Authors: George N Chiduza / Acely Garza-Garcia / Eugenia Almacellas / Stefano De Tito / Valerie E Pye / Alexander R van Vliet / Peter Cherepanov / Sharon A Tooze / ![]() Abstract: Macroautophagy/autophagy is a fundamental aspect of eukaryotic biology, and the autophay-related protein ATG9A is part of the core machinery facilitating this process. In addition to ATG9A ...Macroautophagy/autophagy is a fundamental aspect of eukaryotic biology, and the autophay-related protein ATG9A is part of the core machinery facilitating this process. In addition to ATG9A vertebrates encode ATG9B, a poorly characterized paralog expressed in a subset of tissues. Herein, we characterize the structure of human ATG9B revealing the conserved homotrimeric quaternary structure and explore the conformational dynamics of the protein. Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase. We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A. By establishing the molecular structure and function of ATG9B, our results inform the exploration of niche roles for autophagy machinery in more complex eukaryotes and reveal insights relevant across species. ATG: autophagy related; CHS: cholesteryl hemisuccinate; cryo-EM: single-particle cryogenic electron microscopy; CTF: contrast transfer function: CTH: C- terminal α helix; FSC: fourier shell correlation; HDIR: HORMA domain interacting region; LMNG: lauryl maltose neopentyl glycol; MD: molecular dynamics simulations; MSA: multiple sequence alignment; NBD-PE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl ammonium salt); POPC: palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; RBG: repeating beta groove domain; RMSD: root mean square deviation; SEC: size-exclusion chromatography; TMH: transmembrane helix. | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 78.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.6 KB 20.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 86.9 KB | ||
Masks | ![]() | 83.7 MB | ![]() | |
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() | 74.9 MB 77.8 MB 77.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8poeMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | ATG9B C3 map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: ATG9B C3 DeepEMhancer map
File | emd_17789_additional_1.map | ||||||||||||
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Annotation | ATG9B C3 DeepEMhancer map | ||||||||||||
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Density Histograms |
-Half map: ATG9B C3 half map 2
File | emd_17789_half_map_1.map | ||||||||||||
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Annotation | ATG9B C3 half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: ATG9B C3 half map 1
File | emd_17789_half_map_2.map | ||||||||||||
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Annotation | ATG9B C3 half map 1 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Homotrimer of ATG9B
Entire | Name: Homotrimer of ATG9B |
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Components |
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-Supramolecule #1: Homotrimer of ATG9B
Supramolecule | Name: Homotrimer of ATG9B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 303 KDa |
-Macromolecule #1: Autophagy-related protein 9B
Macromolecule | Name: Autophagy-related protein 9B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 105.667008 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DYKDDDDKDY KDDDDKDYKD DDDKHHHHHH ENLYFQGVSR MGWGGRRRRL GRWGDLGPGS VPLLPMPLPP PPPPSCRGPG GGRISIFSL SPAPHTRSSP SSFSPPTAGP PCSVLQGTGA SQSCHSALPI PATPPTQAQP AMTPASASPS WGSHSTPPLA P ATPTPSQQ ...String: DYKDDDDKDY KDDDDKDYKD DDDKHHHHHH ENLYFQGVSR MGWGGRRRRL GRWGDLGPGS VPLLPMPLPP PPPPSCRGPG GGRISIFSL SPAPHTRSSP SSFSPPTAGP PCSVLQGTGA SQSCHSALPI PATPPTQAQP AMTPASASPS WGSHSTPPLA P ATPTPSQQ CPQDSPGLRV GPLIPEQDYE RLEDCDPEGS QDSPIHGEEQ QPLLHVPEGL RGSWHHIQNL DSFFTKIYSY HQ RNGFACI LLEDVFQLGQ FIFIVTFTTF LLRCVDYNVL FANQPSNHTR PGPFHSKVTL SDAILPSAQC AERIRSSPLL VLL LVLAAG FWLVQLLRSV CNLFSYWDIQ VFYREALHIP PEELSSVPWA EVQSRLLALQ RSGGLCVQPR PLTELDIHHR ILRY TNYQV ALANKGLLPA RCPLPWGGSA AFLSRGLALN VDLLLFRGPF SLFRGGWELP HAYKRSDQRG ALAARWGRTV LLLAA LNLA LSPLVLAWQV LHVFYSHVEL LRREPGALGA RGWSRLARLQ LRHFNELPHE LRARLARAYR PAAAFLRTAA PPAPLR TLL ARQLVFFAGA LFAALLVLTV YDEDVLAVEH VLTAMTALGV TATVARSFIP EEQCQGRAPQ LLLQTALAHM HYLPEEP GP GGRDRAYRQM AQLLQYRAVS LLEELLSPLL TPLFLLFWFR PRALEIIDFF HHFTVDVAGV GDICSFALMD VKRHGHPQ W LSAGQTEASL SQRAEDGKTE LSLMRFSLAH PLWRPPGHSS KFLGHLWGRV QQDAAAWGAT SARGPSTPGV LSNCTSPLP EAFLANLFVH PLLPPRDLSP TAPCPAAATA SLLASISRIA QDPSSVSPGG TGGQKLAQLP ELASAEMSLH VIYLHQLHQQ QQQQEPWGE AAASILSRPC SSPSQPPSPD EEKPSWSSDG SSPASSPRQQ WGTQKARNLF PGGFQVTTDT QKEPDRASCT D UniProtKB: Autophagy-related protein 9B |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 8.5 Details: 20 mM Tris-HCl, pH 8.5; 200 mM NaCl; 1 mM TCEP; 10% glycerol supplemented with 0.001% w/v lauryl maltose neopentyl glycol and 0.0002% w/v cholesteryl hemisuccinate |
Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 50 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 37217 / Average exposure time: 1.2 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 46296 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: OTHER / Target criteria: Cross-correlation coeffecient |
Output model | ![]() PDB-8poe: |