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- EMDB-6075: Reconstruction of the N-terminal domain of C. elegans TFG -

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Basic information

Entry
Database: EMDB / ID: EMD-6075
TitleReconstruction of the N-terminal domain of C. elegans TFG
Map dataReconstruction of the N-terminal domain of C. elegans TFG
Sample
  • Sample: N-terminal domain of C. elegans TFG
  • Organelle or cellular component: TFG
KeywordsTFG / COPII / Sec16 / secretory pathway
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 30.0 Å
AuthorsJohnson A / Bhattacharya N / Hanna M / Schuh AL / Pennington JG / Otegui MS / Stagg SM / Audhya A
CitationJournal: EMBO J / Year: 2015
Title: TFG clusters COPII-coated transport carriers and promotes early secretory pathway organization.
Authors: Adam Johnson / Nilakshee Bhattacharya / Michael Hanna / Janice G Pennington / Amber L Schuh / Lei Wang / Marisa S Otegui / Scott M Stagg / Anjon Audhya /
Abstract: In mammalian cells, cargo-laden secretory vesicles leave the endoplasmic reticulum (ER) en route to ER-Golgi intermediate compartments (ERGIC) in a manner dependent on the COPII coat complex. We ...In mammalian cells, cargo-laden secretory vesicles leave the endoplasmic reticulum (ER) en route to ER-Golgi intermediate compartments (ERGIC) in a manner dependent on the COPII coat complex. We report here that COPII-coated transport carriers traverse a submicron, TFG (Trk-fused gene)-enriched zone at the ER/ERGIC interface. The architecture of TFG complexes as determined by three-dimensional electron microscopy reveals the formation of flexible, octameric cup-like structures, which are able to self-associate to generate larger polymers in vitro. In cells, loss of TFG function dramatically slows protein export from the ER and results in the accumulation of COPII-coated carriers throughout the cytoplasm. Additionally, the tight association between ER and ERGIC membranes is lost in the absence of TFG. We propose that TFG functions at the ER/ERGIC interface to locally concentrate COPII-coated transport carriers and link exit sites on the ER to ERGIC membranes. Our findings provide a new mechanism by which COPII-coated carriers are retained near their site of formation to facilitate rapid fusion with neighboring ERGIC membranes upon uncoating, thereby promoting interorganellar cargo transport.
History
DepositionAug 28, 2014-
Header (metadata) releaseSep 24, 2014-
Map releaseSep 2, 2015-
UpdateSep 2, 2015-
Current statusSep 2, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.74
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.74
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6075.jpg

Downloads & links

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Map

FileDownload / File: emd_6075.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the N-terminal domain of C. elegans TFG
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 112 pix.
= 168. Å		1.5 Å/pix.
x 112 pix.
= 168. Å		1.5 Å/pix.
x 112 pix.
= 168. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.74 / Movie #1: 0.74
Minimum - Maximum-3.11628175 - 3.35940194
Average (Standard dev.)-0.00824904 (±0.45885888)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-56-56-56
Dimensions112112112
Spacing112112112
CellA=B=C: 168.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.51.51.5
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z168.000168.000168.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-56-56-56
NC/NR/NS112112112
D min/max/mean-3.1163.359-0.008

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Supplemental data

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Sample components

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Entire : N-terminal domain of C. elegans TFG

EntireName: N-terminal domain of C. elegans TFG
Components
  • Sample: N-terminal domain of C. elegans TFG
  • Organelle or cellular component: TFG

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Supramolecule #1000: N-terminal domain of C. elegans TFG

SupramoleculeName: N-terminal domain of C. elegans TFG / type: sample / ID: 1000 / Oligomeric state: octamer / Number unique components: 1
Molecular weightTheoretical: 1.4 MDa

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Supramolecule #1: TFG

SupramoleculeName: TFG / type: organelle_or_cellular_component / ID: 1 / Number of copies: 8 / Oligomeric state: octamer / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 1.4 MDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6 / Details: 20 mM HEPES, 100 mM NaCl
StainingType: NEGATIVE / Details: Stained with 2% uranyl formate
GridDetails: carbon grids
VitrificationCryogen name: NITROGEN / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TITAN
Specialist opticsEnergy filter - Name: FEI
DateJun 6, 2012
Image recordingCategory: FILM / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Scanner: TEMSCAN
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 37000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle min: -55

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Image processing

DetailsRCT
CTF correctionDetails: whole image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: MRC, EMAN / Number images used: 30000

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