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- PDB-7b6r: Drosophila melanogaster TRAPPIII partial complex: core plus C8 an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7b6r | |||||||||
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Title | Drosophila melanogaster TRAPPIII partial complex: core plus C8 and C11 attached region | |||||||||
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![]() | EXOCYTOSIS / Golgi / GEFS / Rab1 / TRAPP | |||||||||
Function / homology | ![]() COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / dsRNA transport / cis-Golgi network membrane / Golgi vesicle transport / Neutrophil degranulation ...COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / dsRNA transport / cis-Golgi network membrane / Golgi vesicle transport / Neutrophil degranulation / intra-Golgi vesicle-mediated transport / cis-Golgi network / protein secretion / intracellular transport / long-term memory / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / trans-Golgi network / spermatogenesis / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
![]() | Galindo, A. / Munro, S. / Planelles-Herrero, V.J. / Degliesposti, G. | |||||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 394.5 KB | Display | ![]() |
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PDB format | ![]() | 325.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1002.2 KB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 81.9 KB | Display | |
Data in CIF | ![]() | 120.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12056MC ![]() 7b6dC ![]() 7b6eC ![]() 7b6hC ![]() 7b6xC ![]() 7b6yC ![]() 7b6zC ![]() 7b70C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 4 molecules ADGJ
#1: Protein | Mass: 35409.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: l(3)76BDm, Dmel\CG8793, l(3)76BDm-RA, l(3)L3809, TRAPPC8, CG8793, Dmel_CG8793 Production host: ![]() References: UniProt: Q9VW22 |
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#4: Protein | Mass: 17597.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Trs33, BcDNA:RH37427, Dmel\CG6196, dTrs33, TRAPPC6, Trs33p, CG6196, Dmel_CG6196 Production host: ![]() References: UniProt: Q9VF82 |
#7: Protein | Mass: 16669.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() References: UniProt: Q9VUZ1 |
#9: Protein | Mass: 15511.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() References: UniProt: A1Z8I0 |
-Trafficking protein particle complex ... , 5 types, 6 molecules BCIEFH
#2: Protein | Mass: 81847.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: gry, Dmel\CG17569, gryz, l(3)63Bd, TRAPPC11, CG17569, Dmel_CG17569 Production host: ![]() References: UniProt: Q8IRE3 | ||||||
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#3: Protein | Mass: 20492.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Bet3, BET3, Bet3p, dBet3, Dmel\CG3911, TRAPPC3, CG3911, Dmel_CG3911 Production host: ![]() References: UniProt: Q9VSY8 #5: Protein | | Mass: 16990.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Bet5, BET5, Bet5p, CG1359-RA, Dmel\CG1359, TRAPPC1, CG1359, Dmel_CG1359 Production host: ![]() References: UniProt: Q9VA95 #6: Protein | | Mass: 24736.486 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Trs23, CG9298-RA, Dmel\CG9298, TRAPPC4, TRS23, Trs23p, CG9298, Dmel_CG9298 Production host: ![]() References: UniProt: Q9VLI9 #8: Protein | | Mass: 22371.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Trs31, Dmel\CG10153, TRAPPC5, Trs31p, CG10153, Dmel_CG10153 Production host: ![]() References: UniProt: Q7K2Q8 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: TRAPPIII & TRAPPII Subcomplex: TRAPPCore / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.5455 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||
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 |
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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: ![]() |
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 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1601314 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 353400 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 214.4 / Protocol: OTHER / Space: REAL |