+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22928 | |||||||||||||||||||||||||||||||||
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Title | Structure of the yeast TRAPPIII-Ypt1(Rab1) complex | |||||||||||||||||||||||||||||||||
Map data | Unsharpened reconstruction | |||||||||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information pre-mRNA catabolic process / autophagy of peroxisome / Cvt vesicle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / TRAPPI protein complex / SNARE complex disassembly ...pre-mRNA catabolic process / autophagy of peroxisome / Cvt vesicle assembly / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / Golgi vesicle budding / RAB geranylgeranylation / TRAPPI protein complex / SNARE complex disassembly / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPII-coated vesicle budding / COPII-mediated vesicle transport / cytoplasm to vacuole targeting by the Cvt pathway / intra-Golgi vesicle-mediated transport / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / Golgi stack / cis-Golgi network / protein-containing complex localization / endocytic recycling / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phagophore assembly site / reticulophagy / retrograde transport, endosome to Golgi / cis-Golgi network membrane / SNARE complex assembly / sporulation resulting in formation of a cellular spore / autophagosome assembly / positive regulation of macroautophagy / chromosome organization / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / Neutrophil degranulation / SNARE binding / meiotic cell cycle / macroautophagy / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle / protein-containing complex assembly / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||||||||||||||||||||
Authors | Joiner AMN / Phillips BP / Miller EA / Fromme JC | |||||||||||||||||||||||||||||||||
Funding support | United States, United Kingdom, 10 items
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Citation | Journal: EMBO J / Year: 2021 Title: Structural basis of TRAPPIII-mediated Rab1 activation. Authors: Aaron Mn Joiner / Ben P Phillips / Kumar Yugandhar / Ethan J Sanford / Marcus B Smolka / Haiyuan Yu / Elizabeth A Miller / J Christopher Fromme / Abstract: The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII ...The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII complex. Here, we report the 3.7 Å cryo-EM structure of the Saccharomyces cerevisiae TRAPPIII complex bound to its substrate Rab1/Ypt1. The structure reveals the binding site for the Rab1/Ypt1 hypervariable domain, leading to a model for how the complex interacts with membranes during the activation reaction. We determined that stable membrane binding by the TRAPPIII complex is required for robust activation of Rab1/Ypt1 in vitro and in vivo, and is mediated by a conserved amphipathic α-helix within the regulatory Trs85 subunit. Our results show that the Trs85 subunit serves as a membrane anchor, via its amphipathic helix, for the entire TRAPPIII complex. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes. | |||||||||||||||||||||||||||||||||
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_22928.map.gz | 71.1 MB | EMDB map data format | |
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Header (meta data) | emd-22928-v30.xml emd-22928.xml | 39.8 KB 39.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22928_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_22928.png | 134.8 KB | ||
Masks | emd_22928_msk_1.map | 91.1 MB | Mask map | |
Others | emd_22928_additional_1.map.gz emd_22928_additional_2.map.gz emd_22928_additional_3.map.gz emd_22928_additional_4.map.gz emd_22928_half_map_1.map.gz emd_22928_half_map_2.map.gz | 3.1 MB 5.4 MB 4.8 MB 4.5 MB 71.3 MB 71.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22928 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22928 | HTTPS FTP |
-Related structure data
Related structure data | 7kmtMC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22928.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unsharpened reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.378 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_22928_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: RESOLVE Density Modified Map
File | emd_22928_additional_1.map | ||||||||||||
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Annotation | RESOLVE Density Modified Map | ||||||||||||
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Density Histograms |
-Additional map: PostProcessed (sharpened) masked map
File | emd_22928_additional_2.map | ||||||||||||
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Annotation | PostProcessed (sharpened) masked map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Trs85-focused locally refined map (sharpened)
File | emd_22928_additional_3.map | ||||||||||||
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Annotation | Trs85-focused locally refined map (sharpened) | ||||||||||||
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Density Histograms |
-Additional map: Trs33-focused locally refined map (sharpened)
File | emd_22928_additional_4.map | ||||||||||||
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Annotation | Trs33-focused locally refined map (sharpened) | ||||||||||||
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Density Histograms |
-Half map: half map 1, used for model refinement
File | emd_22928_half_map_1.map | ||||||||||||
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Annotation | half map 1, used for model refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2, used for model validation
File | emd_22928_half_map_2.map | ||||||||||||
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Annotation | half map 2, used for model validation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : TRAPPIII-Ypt1 complex
+Supramolecule #1: TRAPPIII-Ypt1 complex
+Macromolecule #1: Trafficking protein particle complex subunit 23
+Macromolecule #2: Trafficking protein particle complex subunit 31
+Macromolecule #3: Trafficking protein particle complex subunit BET5
+Macromolecule #4: Trafficking protein particle complex subunit BET3
+Macromolecule #5: Trafficking protein particle complex subunit 33
+Macromolecule #6: Trafficking protein particle complex subunit 20
+Macromolecule #7: GTP-binding protein YPT1
+Macromolecule #8: Trafficking protein particle complex III-specific subunit 85
+Macromolecule #9: PALMITIC ACID
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: GLOW DISCHARGE | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Either 0.02% Tween-20 or 0.025% amphipol A8-35 was added before application of the sample to the grid.. |
-Electron microscopy #1
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Microscopy ID | 1 |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Electron microscopy #1~
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 |
Microscopy ID | 1 |
Image recording | Image recording ID: 2 / Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 20.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #1~~
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 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Microscopy ID | 1 |
Image recording | Image recording ID: 3 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |