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- EMDB-26249: Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focus... -
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Open data
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Basic information
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Title | Yeast TRAPPII-Rab11/Ypt32 complex in the closed/open state (focused refinement of central region of the closed monomer) | |||||||||
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![]() | complex / GTPase / Guanosine Exchange Factor / GEF / PROTEIN TRANSPORT | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Bagde SR / Fromme JC | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 192.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.3 KB 21.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 121.3 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 5.1 KB | ||
Others | ![]() ![]() ![]() ![]() | 2.5 MB 12 MB 193.7 MB 193.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 839.7 KB | Display | ![]() |
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Full document | ![]() | 839.3 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Map | ||||||||||||||||||||
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
-Mask #1
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Density Histograms |
-Additional map: RESOLVE Density Modified Map
File | emd_26249_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_26249_additional_2.map | ||||||||||||
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Annotation | PostProcessed (sharpened) masked map | ||||||||||||
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Density Histograms |
-Half map: Half map 1
File | emd_26249_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
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Density Histograms |
-Half map: Half map 2
File | emd_26249_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : TRAPPII complex bound to Rab11/Ypt32
Entire | Name: TRAPPII complex bound to Rab11/Ypt32 |
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Components |
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-Supramolecule #1: TRAPPII complex bound to Rab11/Ypt32
Supramolecule | Name: TRAPPII complex bound to Rab11/Ypt32 / type: complex / ID: 1 / Parent: 0 |
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Molecular weight | Theoretical: 1.1 MDa |
-Supramolecule #2: Rab11/Ypt32
Supramolecule | Name: Rab11/Ypt32 / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: TRAPPII
Supramolecule | Name: TRAPPII / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||
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.. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
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. |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 63000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |