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- EMDB-6076: Reconstruction of the N-terminal domain of human TFG -

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Basic information

Entry
Database: EMDB / ID: EMD-6076
TitleReconstruction of the N-terminal domain of human TFG
Map dataReconstruction of the N-terminal domain of human TFG
Sample
  • Sample: N-terminal domain of human TFG
  • Organelle or cellular component: TFG
KeywordsTFG / COPII / secretory pathway
Biological speciesHomo sapiens (human)
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: 0.75
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.75
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6076.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the N-terminal domain of human TFG
Voxel sizeX=Y=Z: 1.5 Å
Density
Contour LevelBy AUTHOR: 0.75 / Movie #1: 0.75
Minimum - Maximum-2.97305417 - 3.45441437
Average (Standard dev.)0.00076291 (±0.33794355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 216.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.51.51.5
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-2.9733.4540.001

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Supplemental data

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Sample components

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Entire : N-terminal domain of human TFG

EntireName: N-terminal domain of human TFG
Components
  • Sample: N-terminal domain of human TFG
  • Organelle or cellular component: TFG

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Supramolecule #1000: N-terminal domain of human TFG

SupramoleculeName: N-terminal domain of human TFG / type: sample / ID: 1000 / Oligomeric state: octamer / Number unique components: 1

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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: Homo sapiens (human) / synonym: human / Location in cell: cytoplasm

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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 KRIOS
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle min: -55
DateJun 6, 2012
Image recordingCategory: FILM / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Scanner: TEMSCAN / Number real images: 629
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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: 18000

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