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- EMDB-12053: Drosophila melanogaster TRAPP C8, C12 and C13 region map from the... -

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Basic information

Entry
Database: EMDB / ID: EMD-12053
TitleDrosophila melanogaster TRAPP C8, C12 and C13 region map from the TRAPPIII complex
Map datacryoEM map of TRAPPC8, C12 and C13 region of the TRAPPIII complex, obtained after multibody refinement of the whole TRAPPIII map.
Sample
  • Complex: TRAPPIII complex
    • Protein or peptide: FI18195p1
Function / homologyTRAPP 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 speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsGalindo A / Munro S / Planelles-Herrero VJ / Degliesposti G
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 7, 2020-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 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: 0.0275
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0275
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b6e
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b6e
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12053.png

Downloads & links

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Map

FileDownload / File: emd_12053.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM map of TRAPPC8, C12 and C13 region of the TRAPPIII complex, obtained after multibody refinement of the whole TRAPPIII map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 400 pix.
= 499.2 Å		1.25 Å/pix.
x 400 pix.
= 499.2 Å		1.25 Å/pix.
x 400 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.248 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0275 / Movie #1: 0.0275
Minimum - Maximum-0.04898509 - 0.10291098
Average (Standard dev.)-0.0001916462 (±0.0025739244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 499.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2481.2481.248
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z499.200499.200499.200
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0490.103-0.000

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Supplemental data

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Mask #1

Fileemd_12053_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 : TRAPPIII complex

EntireName: TRAPPIII complex
Components
  • Complex: TRAPPIII complex
    • Protein or peptide: FI18195p1

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Supramolecule #1: TRAPPIII complex

SupramoleculeName: TRAPPIII complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Partial model of the TRAPP C8 subunits from the TRAPP C8, C12 and C13 map. Part of the TRAPPIII complex
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)

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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: 35.409438 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 FQKREWS LAEDHIQYTV AKQAYMLKQL EEASRSFAHL LRPGSLQSAQ QQTSFLKEYI QTQNELVKRS

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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

Concentration0.05 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

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.2 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Details32% of the images were acquiring tilted the stage 19 degrees.
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 4 / Number real images: 3671 / Average exposure time: 0.8 sec. / Average electron dose: 30.0 e/Å2
Details: 1190 from the whole dataset were collected with the stage tilted at 19 degrees
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1601314
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 353400
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 302.4
Output model

PDB-7b6e:
Drosophila melanogaster TRAPP C8 subunits region 355 to 661

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