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- EMDB-12058: C8 region from the MiniTRAPPIII complex -

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Basic information

Entry
Database: EMDB / ID: EMD-12058
TitleC8 region from the MiniTRAPPIII complex
Map dataC8 region from the MiniTRAPPIII complex
Sample
  • Complex: TRAPP C8 complex from the Mini TRAPPIII complex.
    • Protein or peptide: FI18195p1
KeywordsGEFs / Golgi / Rab1 / TRAPPIII complex / EXOCYTOSIS
Function / homology
Function and homology information


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
Similarity search - Function
: / TRAPP III complex, Trs85 / ER-Golgi trafficking TRAPP I complex 85 kDa subunit
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 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 8, 2020-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b6y
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b6y
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12058.png

Downloads & links

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Map

FileDownload / File: emd_12058.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC8 region from the MiniTRAPPIII complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 400 pix.
= 502.56 Å		1.26 Å/pix.
x 400 pix.
= 502.56 Å		1.26 Å/pix.
x 400 pix.
= 502.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2564 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.012
Minimum - Maximum-0.031496316 - 0.04769544
Average (Standard dev.)-0.000032843673 (±0.0007607008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 502.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.25641.25641.2564
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z502.560502.560502.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0310.048-0.000

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Supplemental data

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Mask #1

Fileemd_12058_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRAPP C8 complex from the Mini TRAPPIII complex.

EntireName: TRAPP C8 complex from the Mini TRAPPIII complex.
Components
  • Complex: TRAPP C8 complex from the Mini TRAPPIII complex.
    • Protein or peptide: FI18195p1

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Supramolecule #1: TRAPP C8 complex from the Mini TRAPPIII complex.

SupramoleculeName: TRAPP C8 complex from the Mini TRAPPIII complex. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: FI18195p1

MacromoleculeName: FI18195p1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 28.378545 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: DNLRHFVQDY AVRALIPYIE HLVAILAEGV TNKKGVSKSL LSATKRWFVT SKPGAGANNQ NAVIYTNESA ELQTRKLGDL YFMFGHYNL AFQSYHQAKR DFNADSAWQY YAGALEMAAL SAFMLGTAQR KTYDYMEDAI VCYLTVCKLQ QFATRATLLS M ECLKTARL ...String:
DNLRHFVQDY AVRALIPYIE HLVAILAEGV TNKKGVSKSL LSATKRWFVT SKPGAGANNQ NAVIYTNESA ELQTRKLGDL YFMFGHYNL AFQSYHQAKR DFNADSAWQY YAGALEMAAL SAFMLGTAQR KTYDYMEDAI VCYLTVCKLQ QFATRATLLS M ECLKTARL YSEVAKQLIR MTNEESDLRS ALLLEQAAYC FLVTQPPMHR KYAFHIVLAG NRYSRAGQRK HAYRCYRQAY QV FQKREW

UniProtKB: FI18195p1

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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
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 K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3443 / Average exposure time: 12.0 sec. / Average electron dose: 45.6 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: 1242082
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 486758
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-7b6y:
C8(355-600) from the MiniTRAPPIII complex

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