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- EMDB-2088: Structures from COPI-coated vesicles: paired two-corner connection -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2088 | |||||||||
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Title | Structures from COPI-coated vesicles: paired two-corner connection | |||||||||
![]() | Reconstruction of a paired two-corner connection | |||||||||
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![]() | COPI-coated vesicles / subtomogram averaging / membrane trafficking / protein coat / coatomer / COPI | |||||||||
Biological species | unidentified (others) / ![]() ![]() ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 34.0 Å | |||||||||
![]() | Faini M / Prinz S / Beck R / Schorb M / Riches JD / Bacia K / Brugger B / Wieland FT / Briggs JAG | |||||||||
![]() | ![]() Title: The structures of COPI-coated vesicles reveal alternate coatomer conformations and interactions. Authors: Marco Faini / Simone Prinz / Rainer Beck / Martin Schorb / James D Riches / Kirsten Bacia / Britta Brügger / Felix T Wieland / John A G Briggs / ![]() Abstract: Transport between compartments of eukaryotic cells is mediated by coated vesicles. The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human. Structural studies of ...Transport between compartments of eukaryotic cells is mediated by coated vesicles. The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human. Structural studies of COPII and clathrin coats assembled in vitro without membranes suggest that coat components assemble regular cages with the same set of interactions between components. Detailed three-dimensional structures of coated membrane vesicles have not been obtained. Here, we solved the structures of individual COPI-coated membrane vesicles by cryoelectron tomography and subtomogram averaging of in vitro reconstituted budding reactions. The coat protein complex, coatomer, was observed to adopt alternative conformations to change the number of other coatomers with which it interacts and to form vesicles with variable sizes and shapes. This represents a fundamentally different basis for vesicle coat assembly. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
Images | ![]() | 241.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of a paired two-corner connection | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.94 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : paired two-corner connection
Entire | Name: paired two-corner connection |
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Components |
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-Supramolecule #1000: paired two-corner connection
Supramolecule | Name: paired two-corner connection / type: sample / ID: 1000 / Number unique components: 3 |
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-Supramolecule #1: liposome membrane
Supramolecule | Name: liposome membrane / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: unidentified (others) |
-Macromolecule #1: Coatomer complex
Macromolecule | Name: Coatomer complex / type: protein_or_peptide / ID: 1 / Name.synonym: COPI / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 560 KDa |
Recombinant expression | Organism: ![]() |
-Macromolecule #2: Arf1
Macromolecule | Name: Arf1 / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
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Sample preparation
Buffer | pH: 7.5 / Details: 50mM Hepes , 50 mM KOAc, 1 mM MgCl2 |
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Grid | Details: 300 mesh copper grid with holey carbon support, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: OTHER / Method: Hand plunging |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 90 K |
Specialist optics | Energy filter - Name: Gatan GIF 2000 |
Date | May 6, 2011 |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Average electron dose: 60 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.3 µm / Nominal defocus min: 2.3 µm / Nominal magnification: 27500 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Details | CTF correction was performed. Average number of tilts used in the 3D reconstructions: 41. Average tomographic tilt angle increment: 3. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: OTHER / Software - Name: IMOD, TOM, package, Matlab |
CTF correction | Details: CTF multiplication |