+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2432 | |||||||||
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Title | The structure of the COPII coat assembled on membranes | |||||||||
Map data | pos277.mrc | |||||||||
Sample |
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Keywords | COPII / coat / secretion / trafficking / Sec23 / Sec24 / Sar1 / Sec13 / Sec31 / membrane / budding | |||||||||
Function / homology | Function and homology information regulation of COPII vesicle coating / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / SNARE binding / intracellular protein transport ...regulation of COPII vesicle coating / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / SNARE binding / intracellular protein transport / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / zinc ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | electron tomography / cryo EM / negative staining | |||||||||
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 |
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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_2432.map.gz | 4.1 GB | EMDB map data format | |
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Header (meta data) | emd-2432-v30.xml emd-2432.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
Images | EMD-2432.png | 389.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2432 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2432 | HTTPS FTP |
-Validation report
Summary document | emd_2432_validation.pdf.gz | 137.9 KB | Display | EMDB validaton report |
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Full document | emd_2432_full_validation.pdf.gz | 137.1 KB | Display | |
Data in XML | emd_2432_validation.xml.gz | 4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2432 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2432 | HTTPS FTP |
-Related structure data
Related structure data | 2428C 2429C 2430C 2431C 4bziC 4bzjC 4bzkC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2432.map.gz / Format: CCP4 / Size: 4.6 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | pos277.mrc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Cryo-tomogram of COPII-coated membrane
Entire | Name: Cryo-tomogram of COPII-coated membrane |
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Components |
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-Supramolecule #1000: Cryo-tomogram of COPII-coated membrane
Supramolecule | Name: Cryo-tomogram of COPII-coated membrane / type: sample / ID: 1000 / Number unique components: 5 |
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-Macromolecule #1: Sar1p
Macromolecule | Name: Sar1p / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: cytosol/endoplasmic reticulum |
Molecular weight | Experimental: 21.437 KDa / Theoretical: 21.437 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: KBB1012 / Recombinant cell: BL21/DE3 / Recombinant plasmid: pTY40 |
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 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: cytosol/endoplasmic reticulum |
Molecular weight | Experimental: 85.437 KDa / Theoretical: 85.437 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: RSY3764 / Recombinant plasmid: pTKY9 |
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 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: cytosol/endoplasmic reticulum |
Molecular weight | Experimental: 103.577 KDa / Theoretical: 103.577 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: RSY3764 / Recombinant plasmid: pLM129 |
Sequence | UniProtKB: Sec24p InterPro: Sec23/Sec24, trunk domain, Sec23/Sec24 beta-sandwich, Sec23/Sec24, helical domain, Zinc finger, Sec23/Sec24-type |
-Macromolecule #4: Sec13p
Macromolecule | Name: Sec13p / type: protein_or_peptide / ID: 4 / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: cytosol/endoplasmic reticulum |
Molecular weight | Experimental: 20.794 KDa / Theoretical: 20.794 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: RSY1112 / Recombinant plasmid: pNS3141 (6H31/CK1313) |
Sequence | UniProtKB: UNIPROTKB: E7Q6Z3 |
-Macromolecule #5: Sec31p
Macromolecule | Name: Sec31p / type: protein_or_peptide / ID: 5 / Recombinant expression: Yes |
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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 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | electron tomography |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 / Details: HEPES, 50 mM KOAc, 1.2 mM MgCl2 |
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Staining | Type: NEGATIVE / Details: plunge frozen |
Grid | Details: C-flat grids |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-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: FIELD EMISSION GUN |
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 ° / Tilt series - Axis1 - Angle increment: 3 ° |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-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: FIELD EMISSION GUN |
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 ° / Tilt series - Axis1 - Angle increment: 3 ° |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | CTF correction was performed on each projection. Projections aligned based on gold fiducially |
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Final reconstruction | Software - Name: Imod, Raptor / Number images used: 40 |
CTF correction | Details: each projection |