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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2428 | |||||||||
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Title | The structure of the COPII coat assembled on membranes | |||||||||
![]() | Reconstruction of the COPII inner coat assembled on tubular membranes | |||||||||
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![]() | COPII / coat / secretion / trafficking / Sec23 / Sec24 / Sar1 / membrane | |||||||||
Function / homology | ![]() Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / regulation of COPII vesicle coating / positive regulation of ER to Golgi vesicle-mediated transport / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-mediated vesicle transport / nuclear envelope organization / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat ...Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / regulation of COPII vesicle coating / positive regulation of ER to Golgi vesicle-mediated transport / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-mediated vesicle transport / nuclear envelope organization / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / mitochondrial fission / signal sequence binding / fungal-type vacuole membrane / mitochondrial membrane organization / reticulophagy / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / GTPase activator activity / SNARE binding / macroautophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / negative staining / Resolution: 23.0 Å | |||||||||
![]() | Zanetti G / Prinz S / Daum S / Meister A / Schekman R / Bacia K / Briggs JAG | |||||||||
![]() | ![]() 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 |
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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 | ![]() | 913.4 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 16 KB 16 KB | Display Display | ![]() |
Images | ![]() | 132.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 230.6 KB | Display | ![]() |
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Full document | ![]() | 229.8 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bziMC ![]() 2429C ![]() 2430C ![]() 2431C ![]() 2432C ![]() 4bzjC ![]() 4bzkC 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 COPII inner coat assembled on tubular membranes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.3 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 : Sec23/24-Sar1 complex on membrane
Entire | Name: Sec23/24-Sar1 complex on membrane |
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Components |
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-Supramolecule #1000: Sec23/24-Sar1 complex on membrane
Supramolecule | Name: Sec23/24-Sar1 complex on membrane / type: sample / ID: 1000 / Oligomeric state: array of Sec23/24-Sar1 heterotrimers / Number unique components: 4 |
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Molecular weight | Experimental: 210 KDa / Theoretical: 210 KDa |
-Macromolecule #1: Sar1p
Macromolecule | Name: Sar1p / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Oligomeric state: in array / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 21.437 KDa / Theoretical: 21.437 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Small COPII coat GTPase SAR1 / InterPro: Ras GTPase-activating domain, Roc domain |
-Macromolecule #2: Sec23p
Macromolecule | Name: Sec23p / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Oligomeric state: in array / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 85.437 KDa / Theoretical: 85.437 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: UNIPROTKB: E7QAP0 InterPro: Sec23/Sec24, trunk domain, Sec23/Sec24, helical domain, Sec23/Sec24 beta-sandwich, Zinc finger, Sec23/Sec24-type |
-Macromolecule #3: Sec24p
Macromolecule | Name: Sec24p / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Oligomeric state: in array / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 103.577 KDa / Theoretical: 103.577 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Sec24p InterPro: Sec23/Sec24, trunk domain, Sec23/Sec24 beta-sandwich, Sec23/Sec24, helical domain, Zinc finger, Sec23/Sec24-type |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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![]() | subtomogram averaging |
Aggregation state | helical array |
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Sample preparation
Concentration | 0.03 mg/mL |
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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 |
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Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Specialist optics | Energy filter - Name: GATAN GIF 2002 |
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 |
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: 3.2 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 19500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Electron microscopy #2
Microscopy ID | 2 |
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Microscope | FEI TITAN KRIOS |
Specialist optics | Energy filter - Name: GATAN GIF 2002 |
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 |
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: 3.2 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 19500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | see materials and methods in relevant publication |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: OTHER / Software - Name: TOM/AV3, Matlab Details: final map was average of two datasets independently processed Number subtomograms used: 5000 |
CTF correction | Details: each tilted image within tomogram |
Final angle assignment | Details: 0 0 0 in zyz convention |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: ![]() |
Details | the map was combined with 1M2V |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross- correlation |
Output model | ![]() PDB-4bzi: |