+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6075 | |||||||||
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Title | Reconstruction of the N-terminal domain of C. elegans TFG | |||||||||
Map data | Reconstruction of the N-terminal domain of C. elegans TFG | |||||||||
Sample |
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Keywords | TFG / COPII / Sec16 / secretory pathway | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 30.0 Å | |||||||||
Authors | Johnson A / Bhattacharya N / Hanna M / Schuh AL / Pennington JG / Otegui MS / Stagg SM / Audhya A | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6075.map.gz | 1.9 MB | EMDB map data format | |
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Header (meta data) | emd-6075-v30.xml emd-6075.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_6075.jpg | 20.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6075 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6075 | HTTPS FTP |
-Validation report
Summary document | emd_6075_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_6075_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_6075_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6075 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6075 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6075.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the N-terminal domain of C. elegans TFG | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : N-terminal domain of C. elegans TFG
Entire | Name: N-terminal domain of C. elegans TFG |
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Components |
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-Supramolecule #1000: N-terminal domain of C. elegans TFG
Supramolecule | Name: N-terminal domain of C. elegans TFG / type: sample / ID: 1000 / Oligomeric state: octamer / Number unique components: 1 |
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Molecular weight | Theoretical: 1.4 MDa |
-Supramolecule #1: TFG
Supramolecule | Name: TFG / type: organelle_or_cellular_component / ID: 1 / Number of copies: 8 / Oligomeric state: octamer / Recombinant expression: Yes / Database: NCBI |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Molecular weight | Theoretical: 1.4 MDa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 / Details: 20 mM HEPES, 100 mM NaCl |
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Staining | Type: NEGATIVE / Details: Stained with 2% uranyl formate |
Grid | Details: carbon grids |
Vitrification | Cryogen name: NITROGEN / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TITAN |
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Specialist optics | Energy filter - Name: FEI |
Date | Jun 6, 2012 |
Image recording | Category: FILM / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Scanner: TEMSCAN |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 37000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle min: -55 |
-Image processing
Details | RCT |
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CTF correction | Details: whole image |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: MRC, EMAN / Number images used: 30000 |