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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2985 | |||||||||
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Title | The structure of the COPI coat triad | |||||||||
![]() | Reconstruction of the COPI coat triad | |||||||||
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![]() | COPI / coatomer / coated vesicles | |||||||||
Function / homology | ![]() cerebellar Purkinje cell layer maturation / protein localization to cell leading edge / Synthesis of PIPs at the plasma membrane / protein localization to axon / VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / protein localization to Golgi membrane / Golgi localization ...cerebellar Purkinje cell layer maturation / protein localization to cell leading edge / Synthesis of PIPs at the plasma membrane / protein localization to axon / VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / protein localization to Golgi membrane / Golgi localization / COPI-coated vesicle / pancreatic juice secretion / organelle membrane contact site / regulation of Golgi organization / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI-mediated anterograde transport / COPI vesicle coat / positive regulation of mitochondrial fusion / Golgi vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / organelle transport along microtubule / regulation of fatty acid metabolic process / establishment of Golgi localization / Golgi to plasma membrane transport / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Golgi-associated vesicle / pigmentation / positive regulation of mitochondrial fission / endoplasmic reticulum-Golgi intermediate compartment / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / Neutrophil degranulation / adult locomotory behavior / small monomeric GTPase / establishment of localization in cell / macroautophagy / protein kinase C binding / intracellular protein transport / hormone activity / protein transport / growth cone / Golgi membrane / axon / GTPase activity / mRNA binding / neuronal cell body / GTP binding / structural molecule activity / Golgi apparatus / endoplasmic reticulum / extracellular space / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 13.0 Å | |||||||||
![]() | Dodonova SO / Diestelkoetter-Bachert P / von Appen A / Hagen WJH / Beck R / Beck M / Wieland F / Briggs JAG | |||||||||
![]() | ![]() Title: VESICULAR TRANSPORT. A structure of the COPI coat and the role of coat proteins in membrane vesicle assembly. Authors: S O Dodonova / P Diestelkoetter-Bachert / A von Appen / W J H Hagen / R Beck / M Beck / F Wieland / J A G Briggs / ![]() Abstract: Transport of material within cells is mediated by trafficking vesicles that bud from one cellular compartment and fuse with another. Formation of a trafficking vesicle is driven by membrane coats ...Transport of material within cells is mediated by trafficking vesicles that bud from one cellular compartment and fuse with another. Formation of a trafficking vesicle is driven by membrane coats that localize cargo and polymerize into cages to bend the membrane. Although extensive structural information is available for components of these coats, the heterogeneity of trafficking vesicles has prevented an understanding of how complete membrane coats assemble on the membrane. We combined cryo-electron tomography, subtomogram averaging, and cross-linking mass spectrometry to derive a complete model of the assembled coat protein complex I (COPI) coat involved in traffic between the Golgi and the endoplasmic reticulum. The highly interconnected COPI coat structure contradicted the current "adaptor-and-cage" understanding of coated vesicle formation. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.3 KB 15.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 101.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 253.7 KB | Display | ![]() |
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Full document | ![]() | 252.8 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a1uMC ![]() 2986C ![]() 2987C ![]() 2988C ![]() 2989C ![]() 5a1vC ![]() 5a1wC ![]() 5a1xC ![]() 5a1yC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of the COPI coat triad | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.019 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 : COPI coat triad on the membrane
Entire | Name: COPI coat triad on the membrane |
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Components |
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-Supramolecule #1000: COPI coat triad on the membrane
Supramolecule | Name: COPI coat triad on the membrane / type: sample / ID: 1000 Details: The COPI coated vesicles were formed in an in vitro reconstituted budding reaction, which was plunge-frozen without further purification. Number unique components: 2 |
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Molecular weight | Theoretical: 1.4 MDa |
-Macromolecule #1: Coat protein 1
Macromolecule | Name: Coat protein 1 / 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: ![]() ![]() |
Sequence | InterPro: Coatomer subunit alpha, Coatomer beta' subunit (COPB2), Coatomer, epsilon subunit, Coatomer beta subunit (COPB1), Coatomer delta subunit, Coatomer gamma subunit, AP complex, mu/sigma subunit |
-Macromolecule #2: ADP-ribosylation factor 1
Macromolecule | Name: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 2 / Name.synonym: Arf1 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: ADP-ribosylation factor 1 / InterPro: Small GTPase superfamily, ARF type |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 / Details: 50 mM HEPES, 50 mM KAc, 1mM MgCl2 |
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Grid | Details: C-Flat Multihole 3C-50 grids glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Instrument: HOMEMADE PLUNGER Method: The grids were glow discharged for 1 min at 20 mA. 5 ul of 10 nm fiducial gold was added to 40 ul of reaction mix. The reaction mix with the in vitro formed coated vesicles was applied to a ...Method: The grids were glow discharged for 1 min at 20 mA. 5 ul of 10 nm fiducial gold was added to 40 ul of reaction mix. The reaction mix with the in vitro formed coated vesicles was applied to a grid. The grid was blotted for 12 seconds at room temperature before plunging |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 89 K / Max: 91 K / Average: 90 K |
Specialist optics | Energy filter - Name: GATAN GIF 2002 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Feb 7, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN MULTISCAN / Average electron dose: 45 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -45 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: ![]() |
Details | The crystal structure (chains A and B) was fitted into the EM map using global search option in Chimera software. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | ![]() PDB-5a1u: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C |
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Software | Name: ![]() |
Details | The crystal structure (chains A, B, C) was fitted into the EM map using global search option in Chimera software. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | ![]() PDB-5a1u: |
-Atomic model buiding 3
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: ![]() |
Details | The crystal structure (chain A) was fitted into the EM map using in Chimera software. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | ![]() PDB-5a1u: |
-Atomic model buiding 4
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: ![]() |
Details | The crystal structure (chain A) was fitted into the EM map using in Chimera software. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation |
Output model | ![]() PDB-5a1u: |