+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2430 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of the COPII coat assembled on membranes | |||||||||
Map data | sec13/31 outer coat edge left-handed direction | |||||||||
Sample |
| |||||||||
Keywords | COPII / coat / secretion / trafficking / Sec13 / Sec31 | |||||||||
Function / homology | Function and homology information Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / COPII vesicle coat ...Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / mating projection tip / endoplasmic reticulum organization / vacuolar membrane / nucleocytoplasmic transport / positive regulation of TOR signaling / mRNA transport / endoplasmic reticulum exit site / nuclear pore / : / positive regulation of TORC1 signaling / cell periphery / intracellular protein transport / protein import into nucleus / nuclear envelope / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | subtomogram averaging / cryo EM / negative staining / Resolution: 40.0 Å | |||||||||
Authors | Zanetti G / Prinz S / Daum S / Meister A / Schekman R / Bacia K / Briggs JAG | |||||||||
Citation | Journal: Elife / Year: 2013 Title: The structure of the COPII transport-vesicle coat assembled on membranes. Authors: Giulia Zanetti / Simone Prinz / Sebastian Daum / Annette Meister / Randy Schekman / Kirsten Bacia / John A G Briggs / Abstract: Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, ...Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, linking them to the outer COPII components that form a cage around the vesicle. Regulated flexibility in coat architecture is essential for transport of a variety of differently sized cargoes, but structural data on the assembled coat has not been available. We have used cryo-electron tomography and subtomogram averaging to determine the structure of the complete, membrane-assembled COPII coat. We describe a novel arrangement of the outer coat and find that the inner coat can assemble into regular lattices. The data reveal how coat subunits interact with one another and with the membrane, suggesting how coordinated assembly of inner and outer coats can mediate and regulate packaging of vesicles ranging from small spheres to large tubular carriers. DOI:http://dx.doi.org/10.7554/eLife.00951.001. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2430.map.gz | 1.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2430-v30.xml emd-2430.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_2430.png | 46.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2430 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2430 | HTTPS FTP |
-Related structure data
Related structure data | 4bzjMC 2428C 2429C 2431C 2432C 4bziC 4bzkC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_2430.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sec13/31 outer coat edge left-handed direction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Sec13/31 complex (as part of complete COPII assembled on membrane...
Entire | Name: Sec13/31 complex (as part of complete COPII assembled on membrane) edge in left-handed direction |
---|---|
Components |
|
-Supramolecule #1000: Sec13/31 complex (as part of complete COPII assembled on membrane...
Supramolecule | Name: Sec13/31 complex (as part of complete COPII assembled on membrane) edge in left-handed direction type: sample / ID: 1000 / Oligomeric state: heterotetramers of sec13 and sec31 / Number unique components: 2 |
---|---|
Molecular weight | Experimental: 319.236 KDa / Theoretical: 319.236 KDa |
-Macromolecule #1: Sec31
Macromolecule | Name: Sec31 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Oligomeric state: heterotetramer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: cytosol/endoplasmic reticulum |
Molecular weight | Experimental: 138.824 KDa / Theoretical: 138.824 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: RSY1112 / Recombinant plasmid: pNS3141 (6H31/CK1313) |
Sequence | UniProtKB: UNIPROTKB: E7Q1I6 |
-Macromolecule #2: Sec13
Macromolecule | Name: Sec13 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Oligomeric state: heterotetramer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: cytosol/endoplasmic reticulum |
Molecular weight | Experimental: 20.79 KDa / Theoretical: 27.9 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: RSY1112 / Recombinant plasmid: pNS3141 (6H31/CK1313) |
Sequence | UniProtKB: UNIPROTKB: E7Q6Z3 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | helical array |
-Sample preparation
Concentration | 0.03 mg/mL |
---|---|
Buffer | pH: 6.8 / Details: HEPES, 50 mM KOAc, 1.2 mM MgCl2 |
Staining | Type: NEGATIVE / Details: plunge frozen |
Grid | Details: C-flat grids |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy #1
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 19500 |
Specialist optics | Energy filter - Name: GATAN GIF 2002 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Microscopy ID | 1 |
Date | Sep 18, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN MULTISCAN / Number real images: 26 / Average electron dose: 80 e/Å2 / Bits/pixel: 16 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Electron microscopy #2
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 19500 |
Specialist optics | Energy filter - Name: GATAN GIF 2002 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Microscopy ID | 2 |
Date | Jun 19, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN MULTISCAN / Number real images: 26 / Average electron dose: 80 e/Å2 / Bits/pixel: 16 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each tilted image within tomogram |
---|---|
Final angle assignment | Details: 0 0 0 in zyz convention |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: TOM/AV3, Matlab / Number subtomograms used: 182 |
Details | see materials and methods in relevant publication |
-Atomic model buiding 1
Initial model | PDB ID: |
---|---|
Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation |
Output model | PDB-4bzj: |