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- EMDB-12066: Drosophila melnaogaster TRAPPII -

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Basic information

Entry
Database: EMDB / ID: EMD-12066
TitleDrosophila melnaogaster TRAPPII
Map data
Sample
  • Complex: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific subunits
Function / homology
Function and homology information


COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / Golgi vesicle transport / Neutrophil degranulation / cis-Golgi network membrane / cis-Golgi network ...COPII-mediated vesicle transport / RAB GEFs exchange GTP for GDP on RABs / TRAPPI protein complex / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / Golgi vesicle transport / Neutrophil degranulation / cis-Golgi network membrane / cis-Golgi network / intra-Golgi vesicle-mediated transport / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular transport / long-term memory / vesicle-mediated transport / trans-Golgi network / nervous system development / spermatogenesis / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / nucleus / cytoplasm / cytosol
Similarity search - Function
Trafficking protein particle complex subunit 2-like / : / Trafficking protein particle complex subunit 11 / Trafficking protein particle complex subunit 11, C-terminal / Foie gras liver health family 1 / Gryzun, putative Golgi trafficking / TRAPP III complex, Trs85 / ER-Golgi trafficking TRAPP I complex 85 kDa subunit / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region ...Trafficking protein particle complex subunit 2-like / : / Trafficking protein particle complex subunit 11 / Trafficking protein particle complex subunit 11, C-terminal / Foie gras liver health family 1 / Gryzun, putative Golgi trafficking / TRAPP III complex, Trs85 / ER-Golgi trafficking TRAPP I complex 85 kDa subunit / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / Trafficking protein particle complex subunit / Sybindin-like family / Sybindin-like family / TRAPP I complex, subunit 5 / TRAPP complex, Trs33 subunit / Bet3 family / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / NO signalling/Golgi transport ligand-binding domain superfamily / Longin-like domain superfamily
Similarity search - Domain/homology
Trafficking protein particle complex subunit 2-like protein / Trafficking protein particle complex subunit 5 / Trafficking protein particle complex subunit 11 / Trafficking protein particle complex subunit / Trafficking protein particle complex subunit 6B / Trafficking protein particle complex subunit / Trafficking protein particle complex subunit / Probable trafficking protein particle complex subunit 2 / FI18195p1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsGalindo A / Munro S
CitationJournal: 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
DepositionDec 9, 2020-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12066.png

Downloads & links

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Map

FileDownload / File: emd_12066.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 400 pix.
= 525.12 Å		1.31 Å/pix.
x 400 pix.
= 525.12 Å		1.31 Å/pix.
x 400 pix.
= 525.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3128 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0054 / Movie #1: 0.006
Minimum - Maximum-0.023327928 - 0.038620878
Average (Standard dev.)-3.9120096e-05 (±0.0016477513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 525.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31281.31281.3128
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z525.120525.120525.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0230.039-0.000

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Supplemental data

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Sample components

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Entire : MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific s...

EntireName: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific subunits
Components
  • Complex: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific subunits

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Supramolecule #1: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific s...

SupramoleculeName: MiniTRAPPIII: TRAPPIII complex without the C12 and C13 specific subunits
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Molecular weightExperimental: 453 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
50.0 mMHepes-KOH
250.0 mMKAc
1.0 mMDTT
0.005 (v/v)%Igepal C-630
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.001 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 364 / Average exposure time: 0.8 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -0.0025 µm / Nominal defocus min: -0.0015 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 43161
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 4415
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.1)

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