+Open data
-Basic information
Entry | Database: PDB / ID: 7b6z | ||||||
---|---|---|---|---|---|---|---|
Title | TRAPPC11 subunit (1-716) | ||||||
Components | Trafficking protein particle complex subunit 11 | ||||||
Keywords | EXOCYTOSIS / GEFs / Golgi / Rab1 / TRAPPIII complex | ||||||
Function / homology | Function and homology information RAB GEFs exchange GTP for GDP on RABs / TRAPPIII protein complex / Golgi vesicle transport / protein secretion / intracellular transport / long-term memory / Golgi apparatus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å | ||||||
Authors | Galindo, A. / Munro, S. / Planelles-Herrero, V.J. | ||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7b6z.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7b6z.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 7b6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b6z_validation.pdf.gz | 914.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7b6z_full_validation.pdf.gz | 940.8 KB | Display | |
Data in XML | 7b6z_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 7b6z_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/7b6z ftp://data.pdbj.org/pub/pdb/validation_reports/b6/7b6z | HTTPS FTP |
-Related structure data
Related structure data | 12060MC 7b6dC 7b6eC 7b6hC 7b6rC 7b6xC 7b6yC 7b70C C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 81847.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: gry, Dmel\CG17569, gryz, l(3)63Bd, TRAPPC11, CG17569, Dmel_CG17569 Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: Q8IRE3 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TRAPPC11 region from the Mini TRAPPIII complex. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||||||||||
Specimen | Conc.: 0.5 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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2.5 nm / Nominal defocus min: 1.5 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: 12 sec. / Electron dose: 45.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3443 |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1242082 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 486758 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL |