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Yorodumi- EMDB-26254: Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26254 | |||||||||
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Title | Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (composite structure) | |||||||||
Map data | Composite map of TRAPPII-Ypt32 symmetric closed/closed dimer | |||||||||
Sample |
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Function / homology | Function and homology information Anchoring of the basal body to the plasma membrane / beta-glucan biosynthetic process / RAB geranylgeranylation / TRAPPI protein complex / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPII-mediated vesicle transport ...Anchoring of the basal body to the plasma membrane / beta-glucan biosynthetic process / RAB geranylgeranylation / TRAPPI protein complex / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPII-mediated vesicle transport / cytoplasm to vacuole targeting by the Cvt pathway / intra-Golgi vesicle-mediated transport / protein localization to phagophore assembly site / cellular bud neck / cis-Golgi network / protein-containing complex localization / phagophore assembly site / retrograde transport, endosome to Golgi / cis-Golgi network membrane / exocytosis / positive regulation of macroautophagy / chromosome organization / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / Neutrophil degranulation / cell wall organization / macroautophagy / trans-Golgi network / recycling endosome / autophagy / protein transport / protein-containing complex assembly / mitochondrial outer membrane / early endosome / endosome / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) / baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Bagde SR / Fromme JC | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structure of a TRAPPII-Rab11 activation intermediate reveals GTPase substrate selection mechanisms. Authors: Saket R Bagde / J Christopher Fromme / Abstract: Rab1 and Rab11 are essential regulators of the eukaryotic secretory and endocytic recycling pathways. The transport protein particle (TRAPP) complexes activate these guanosine triphosphatases via ...Rab1 and Rab11 are essential regulators of the eukaryotic secretory and endocytic recycling pathways. The transport protein particle (TRAPP) complexes activate these guanosine triphosphatases via nucleotide exchange using a shared set of core subunits. The basal specificity of the TRAPP core is toward Rab1, yet the TRAPPII complex is specific for Rab11. A steric gating mechanism has been proposed to explain TRAPPII counterselection against Rab1. Here, we present cryo-electron microscopy structures of the 22-subunit TRAPPII complex from budding yeast, including a TRAPPII-Rab11 nucleotide exchange intermediate. The Trs130 subunit provides a "leg" that positions the active site distal to the membrane surface, and this leg is required for steric gating. The related TRAPPIII complex is unable to activate Rab11 because of a repulsive interaction, which TRAPPII surmounts using the Trs120 subunit as a "lid" to enclose the active site. TRAPPII also adopts an open conformation enabling Rab11 to access and exit from the active site chamber. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26254.map.gz | 28 MB | EMDB map data format | |
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Header (meta data) | emd-26254-v30.xml emd-26254.xml | 34.9 KB 34.9 KB | Display Display | EMDB header |
Images | emd_26254.png | 84.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26254 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26254 | HTTPS FTP |
-Related structure data
Related structure data | 7u05MC 7u06C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26254.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map of TRAPPII-Ypt32 symmetric closed/closed dimer | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.432 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : TRAPPII complex bound to Rab11/Ypt32
+Supramolecule #1: TRAPPII complex bound to Rab11/Ypt32
+Macromolecule #1: Trafficking protein particle complex II-specific subunit 130
+Macromolecule #2: Trafficking protein particle complex II-specific subunit 65
+Macromolecule #3: TRAPP-associated protein TCA17
+Macromolecule #4: Trafficking protein particle complex subunit 33
+Macromolecule #5: Trafficking protein particle complex subunit BET3
+Macromolecule #6: Trafficking protein particle complex subunit BET5
+Macromolecule #7: Trafficking protein particle complex subunit 23
+Macromolecule #8: Trafficking protein particle complex subunit 31
+Macromolecule #9: Trafficking protein particle complex subunit 20
+Macromolecule #10: GTP-binding protein YPT32/YPT11
+Macromolecule #11: Trafficking protein particle complex II-specific subunit 130
+Macromolecule #12: Trafficking protein particle complex II-specific subunit 120
+Macromolecule #13: Trafficking protein particle complex II-specific subunit 65
+Macromolecule #14: PALMITIC ACID
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.6 mg/mL | ||||||||||||
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Buffer | pH: 8 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 / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: The sample was incubated on the grid for 10 seconds followed by blotting for 5 seconds before plunging in liquid ethane.. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 63000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 3 / Number real images: 4998 / Average exposure time: 3.5 sec. / Average electron dose: 53.0 e/Å2 / Details: Images were collected as 50 frame movies. |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 979187 | ||||||
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CTF correction | Software:
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Startup model | Type of model: INSILICO MODEL In silico model: Used Ab-initio Reconstruction job in cryoSPARC to generate starting map. | ||||||
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0) | ||||||
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) | ||||||
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX Details: The composite map was generated by combining the consensus dimer map (EMD-26221) with focused refinement maps deposited in the entries EMD-26223, EMD-26224. EMD-26225, EMD-26226, EMD-26227, ...Details: The composite map was generated by combining the consensus dimer map (EMD-26221) with focused refinement maps deposited in the entries EMD-26223, EMD-26224. EMD-26225, EMD-26226, EMD-26227, EMD-26228, EMD-26229, EMD-26230, EMD-26231 and EMD-26232 using Combine Focused Maps in Phenix. Number images used: 369488 |