+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3724 | |||||||||
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Title | The structure of the COPI coat linkage IV | |||||||||
Map data | The structure of the COPI coat linkage IV | |||||||||
Sample |
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Function / homology | Function and homology information cerebellar Purkinje cell layer maturation / protein localization to cell leading edge / protein localization to axon / VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Golgi localization / COPI-coated vesicle / pancreatic juice secretion ...cerebellar Purkinje cell layer maturation / protein localization to cell leading edge / protein localization to axon / VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Golgi localization / COPI-coated vesicle / pancreatic juice secretion / COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI-mediated anterograde transport / Golgi vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / organelle transport along microtubule / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane transport / establishment of Golgi localization / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / pigmentation / Golgi-associated vesicle / protein secretion / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / Neutrophil degranulation / adult locomotory behavior / small monomeric GTPase / protein kinase C binding / establishment of localization in cell / macroautophagy / intracellular protein transport / hormone activity / protein transport / growth cone / axon / Golgi membrane / mRNA binding / intracellular membrane-bounded organelle / GTPase activity / neuronal cell body / structural molecule activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular space / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 17.3 Å | |||||||||
Authors | Dodonova SO / Aderhold P / Kopp J / Ganeva I / Roehling S / Hagen WJH / Sinning I / Wieland F / Briggs JAG | |||||||||
Citation | Journal: Elife / Year: 2017 Title: 9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments. Authors: Svetlana O Dodonova / Patrick Aderhold / Juergen Kopp / Iva Ganeva / Simone Röhling / Wim J H Hagen / Irmgard Sinning / Felix Wieland / John A G Briggs / Abstract: COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that ...COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that recruits the coatomer complex to the membrane, triggering polymerization and budding. The vesicle uncoats before fusion with a target membrane. Coat components are structurally conserved between COPI and clathrin/adaptor proteins. Using cryo-electron tomography and subtomogram averaging, we determined the structure of the COPI coat assembled on membranes in vitro at 9 Å resolution. We also obtained a 2.57 Å resolution crystal structure of βδ-COP. By combining these structures we built a molecular model of the coat. We additionally determined the coat structure in the presence of ArfGAP proteins that regulate coat dissociation. We found that Arf1 occupies contrasting molecular environments within the coat, leading us to hypothesize that some Arf1 molecules may regulate vesicle assembly while others regulate coat disassembly. | |||||||||
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_3724.map.gz | 33.8 MB | EMDB map data format | |
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Header (meta data) | emd-3724-v30.xml emd-3724.xml | 28.1 KB 28.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3724_fsc.xml | 8.1 KB | Display | FSC data file |
Images | emd_3724.png | 127.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3724 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3724 | HTTPS FTP |
-Related structure data
Related structure data | 5nzvMC 3720C 3721C 3722C 3723C 5mu7C 5nzrC 5nzsC 5nztC 5nzuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3724.map.gz / Format: CCP4 / Size: 36.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The structure of the COPI coat linkage IV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.78 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 : The structure of the COPI coat leaf
+Supramolecule #1: The structure of the COPI coat leaf
+Supramolecule #2: COPI coat complex
+Supramolecule #3: ADP-ribosylation factor 1
+Macromolecule #1: Coatomer subunit alpha
+Macromolecule #2: Coatomer subunit epsilon
+Macromolecule #3: Coatomer subunit beta
+Macromolecule #4: Coatomer subunit beta'
+Macromolecule #5: Coatomer subunit delta
+Macromolecule #6: ADP-ribosylation factor 1
+Macromolecule #7: Coatomer subunit gamma-1
+Macromolecule #8: Coatomer subunit zeta-1
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.4 Component:
Details: Protein-A conjugated 10 nm gold was added to the reaction mix in 1:6 volume ratio before plunge-freezing | ||||||||||||
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Grid | Model: C-flat / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Protochips C-flat MultiHole 20 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 296 K / Instrument: HOMEMADE PLUNGER Details: The sample was applied onto glow-discharged (30 sec, 20 mA) C-flat (Protochips Inc.) multihole grids. The grids were blotted from the back side for 11 seconds at room temperature in a ...Details: The sample was applied onto glow-discharged (30 sec, 20 mA) C-flat (Protochips Inc.) multihole grids. The grids were blotted from the back side for 11 seconds at room temperature in a chamber at 85% humidity and plunge-frozen into liquid ethane using a manual plunger.. | ||||||||||||
Details | COPI-coated vesicles were produced in vitro by incubating coatomer, Arf1, GTPgS, ARNO and GUVs in a total volume of 40 ul for 30 minutes at 37C |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 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: 5.0 µm / Nominal defocus min: 2.5 µm |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | Tomographic tilt series were acquired with the dose-symmetric tilt-scheme (Hagen et al., J Struct Biol. 2017) |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-5 / Number grids imaged: 1 / Average electron dose: 2.0 e/Å2 Details: Each of the images in the tilt series was low-pass filtered according to the electron-dose acquired by the sample (Grant and Grigorieff, 2015). |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
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Output model | PDB-5nzv: |