+Open data
-Basic information
Entry | Database: PDB / ID: 7b6e | |||||||||
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Title | Drosophila melanogaster TRAPP C8 subunits region 355 to 661 | |||||||||
Components | FI18195p1 | |||||||||
Keywords | EXOCYTOSIS / Golgi / GEFS / Rab1 / TRAPP | |||||||||
Function / homology | TRAPP III complex, Trs85 / ER-Golgi trafficking TRAPP I complex 85 kDa subunit / RAB GEFs exchange GTP for GDP on RABs / TRAPPIII protein complex / TRAPP complex / Golgi vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / Golgi apparatus / FI18195p1 Function and homology information | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Galindo, A. / Munro, S. / Planelles-Herrero, V.J. / Degliesposti, G. | |||||||||
Citation | Journal: EMBO J / Year: 2021 Title: Cryo-EM structure of metazoan TRAPPIII, the multi-subunit complex that activates the GTPase Rab1. Authors: Antonio Galindo / Vicente J Planelles-Herrero / Gianluca Degliesposti / Sean Munro / Abstract: The TRAPP complexes are nucleotide exchange factors that play essential roles in membrane traffic and autophagy. TRAPPII activates Rab11, and TRAPPIII activates Rab1, with the two complexes sharing a ...The TRAPP complexes are nucleotide exchange factors that play essential roles in membrane traffic and autophagy. TRAPPII activates Rab11, and TRAPPIII activates Rab1, with the two complexes sharing a core of small subunits that affect nucleotide exchange but being distinguished by specific large subunits that are essential for activity in vivo. Crystal structures of core subunits have revealed the mechanism of Rab activation, but how the core and the large subunits assemble to form the complexes is unknown. We report a cryo-EM structure of the entire Drosophila TRAPPIII complex. The TRAPPIII-specific subunits TRAPPC8 and TRAPPC11 hold the catalytic core like a pair of tongs, with TRAPPC12 and TRAPPC13 positioned at the joint between them. TRAPPC2 and TRAPPC2L link the core to the two large arms, with the interfaces containing residues affected by disease-causing mutations. The TRAPPC8 arm is positioned such that it would contact Rab1 that is bound to the core, indicating how the arm could determine the specificity of the complex. A lower resolution structure of TRAPPII shows a similar architecture and suggests that the TRAPP complexes evolved from a single ur-TRAPP. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7b6e.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b6e.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 7b6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b6e_validation.pdf.gz | 995.4 KB | Display | wwPDB validaton report |
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Full document | 7b6e_full_validation.pdf.gz | 1008.1 KB | Display | |
Data in XML | 7b6e_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 7b6e_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/7b6e ftp://data.pdbj.org/pub/pdb/validation_reports/b6/7b6e | HTTPS FTP |
-Related structure data
Related structure data | 12053MC 7b6dC 7b6hC 7b6rC 7b6xC 7b6yC 7b6zC 7b70C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 35409.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: l(3)76BDm, Dmel\CG8793, l(3)76BDm-RA, l(3)L3809, TRAPPC8, CG8793, Dmel_CG8793 Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: Q9VW22 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TRAPPIII complex / Type: COMPLEX Details: Partial model of the TRAPP C8 subunits from the TRAPP C8, C12 and C13 map. Part of the TRAPPIII complex Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Drosophila melanogaster (fruit fly) | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS Details: 32% of the images were acquiring tilted the stage 19 degrees. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 75000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.8 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 3671 Details: 1190 from the whole dataset were collected with the stage tilted at 19 degrees |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1601314 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 353400 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 302.4 / Protocol: OTHER / Space: REAL |