+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5269 | |||||||||
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Title | 3D reconstruction of yeast coatomer | |||||||||
Map data | 3D reconstruction of yeast coatomer | |||||||||
Sample |
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Keywords | coatomer / COP1 vesicle / vesicular trafficking / coat complex | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 36.0 Å | |||||||||
Authors | Yip CK / Walz T | |||||||||
Citation | Journal: J Mol Biol / Year: 2011 Title: Molecular structure and flexibility of the yeast coatomer as revealed by electron microscopy. Authors: Calvin K Yip / Thomas Walz / Abstract: Coat protein complex I (COPI)-coated vesicles, one of three major types of vesicular carriers in the cell, mediate the early secretory pathway and retrograde transport from the Golgi to the ...Coat protein complex I (COPI)-coated vesicles, one of three major types of vesicular carriers in the cell, mediate the early secretory pathway and retrograde transport from the Golgi to the endoplasmic reticulum. COPI vesicles are generated through activation of the regulatory GTPase Arf1 at the donor membrane and the subsequent recruitment of coatomer, a coat protein complex consisting of seven stably associated components. Coatomer functions in binding and sequestering cargo molecules and assembles into a polymeric protein shell that encompasses the surface of COPI vesicles. Little is known about the structural properties of this heptameric complex. We have isolated native yeast coatomer and examined its structure and subunit organization by single-particle electron microscopy. Our analyses provide the first three-dimensional picture of the complete coatomer and reveal substantial conformational flexibility likely to be critical for its scaffolding function. | |||||||||
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_5269.map.gz | 2.6 MB | EMDB map data format | |
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Header (meta data) | emd-5269-v30.xml emd-5269.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_5269_1.png | 25.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5269 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5269 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5269.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D reconstruction of yeast coatomer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.2 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 : Yeast coatomer complex
Entire | Name: Yeast coatomer complex |
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Components |
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-Supramolecule #1000: Yeast coatomer complex
Supramolecule | Name: Yeast coatomer complex / type: sample / ID: 1000 / Oligomeric state: one heteroheptamer / Number unique components: 7 |
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Molecular weight | Theoretical: 570 KDa |
-Macromolecule #1: Cop1
Macromolecule | Name: Cop1 / type: protein_or_peptide / ID: 1 / Name.synonym: alpha / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast / Cell: yeast / Location in cell: cytoplasm |
Molecular weight | Theoretical: 136 KDa |
-Macromolecule #2: Sec26
Macromolecule | Name: Sec26 / type: protein_or_peptide / ID: 2 / Name.synonym: beta / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast / Cell: yeast / Location in cell: cytoplasm |
Molecular weight | Theoretical: 109 KDa |
-Macromolecule #3: Sec27
Macromolecule | Name: Sec27 / type: protein_or_peptide / ID: 3 / Name.synonym: beta' / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast / Cell: yeast / Location in cell: cytoplasm |
Molecular weight | Theoretical: 109 KDa |
-Macromolecule #4: Sec21
Macromolecule | Name: Sec21 / type: protein_or_peptide / ID: 4 / Name.synonym: gamma / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast / Cell: yeast / Location in cell: cytoplasm |
Molecular weight | Theoretical: 105 KDa |
-Macromolecule #5: Ret2
Macromolecule | Name: Ret2 / type: protein_or_peptide / ID: 5 / Name.synonym: delta / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast / Cell: yeast / Location in cell: cytoplasm |
Molecular weight | Theoretical: 61 KDa |
-Macromolecule #6: Sec28
Macromolecule | Name: Sec28 / type: protein_or_peptide / ID: 6 / Name.synonym: epsilon / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast / Cell: yeast / Location in cell: cytoplasm |
Molecular weight | Theoretical: 34 KDa |
-Macromolecule #7: Ret3
Macromolecule | Name: Ret3 / type: protein_or_peptide / ID: 7 / Name.synonym: zeta / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast / Cell: yeast / Location in cell: cytoplasm |
Molecular weight | Theoretical: 22 KDa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 8 Details: 20 mM Tris, pH 8.0, 150 mM NaCl, 10% glycerol, 0.005% NP40, 0.5 mM DTT |
Staining | Type: NEGATIVE Details: Protein solution was adsorbed onto grids for 30 seconds before staining with 0.75% uranyl formate |
Vitrification | Cryogen name: NITROGEN / Chamber temperature: 100 K / Instrument: OTHER / Method: Manual plunging into liquid nitrogen |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 51159 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.4 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: OTHER / Tilt angle max: 50 |
Temperature | Average: 100 K |
Details | Low dose imaging, same specimen area imaged twice |
Date | Mar 1, 2009 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 21 µm |
Tilt angle min | 0 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final angle assignment | Details: SPIDER:theta 45 degrees, phi 45 degrees |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 36.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: Final map is filtered to 36 Angstroms resolution |