+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1784 | |||||||||
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Title | The Structure of a COPII Tubule | |||||||||
Map data | This is a raw Tomogram of a Sec1331 Tubule (suggested contour level 60.1) | |||||||||
Sample |
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Keywords | Secretory pathway / Cryo-electron microscopy / Cryo-electron tomography / COPII / cargo / Subvolume averaging | |||||||||
Function / homology | intracellular protein transport / WD40 repeat Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM / Resolution: 85.0 Å | |||||||||
Authors | ODonnell J / Maddox K / Stagg S | |||||||||
Citation | Journal: J Struct Biol / Year: 2011 Title: The structure of a COPII tubule. Authors: Jason O'Donnell / Kerry Maddox / Scott Stagg / Abstract: Nearly a third of all eukaryotic proteins are transported from the ER to the Golgi apparatus through the secretory pathway using COPII coated vesicles. Evidence suggests that this transport occurs ...Nearly a third of all eukaryotic proteins are transported from the ER to the Golgi apparatus through the secretory pathway using COPII coated vesicles. Evidence suggests that this transport occurs via 500-900 Å vesicles that bud from the ER membrane. It has been shown that procollagen molecules utilize the COPII proteins for transport, but it is unclear how the COPII coat can accommodate these ∼3000 Å long molecules. We now present a cryogenic electron tomographic reconstruction of a Sec13/31 tubule that is approximately 3300 Å long containing a hollow cylindrical interior that is 300 Å in diameter, dimensions that are consistent with those that are required to encapsulate a procollagen molecule wrapped in a membrane and accessory COPII components. This structure suggests a novel mechanism that the COPII coat may employ to transport elongated cargo. | |||||||||
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_1784.map.gz | 221.2 MB | EMDB map data format | |
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Header (meta data) | emd-1784-v30.xml emd-1784.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | 1784.jpg | 747.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1784 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1784 | HTTPS FTP |
-Validation report
Summary document | emd_1784_validation.pdf.gz | 230.6 KB | Display | EMDB validaton report |
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Full document | emd_1784_full_validation.pdf.gz | 229.7 KB | Display | |
Data in XML | emd_1784_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1784 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1784 | HTTPS FTP |
-Related structure data
Related structure data | 1785C 1786C 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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-Map
File | Download / File: emd_1784.map.gz / Format: CCP4 / Size: 232.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a raw Tomogram of a Sec1331 Tubule (suggested contour level 60.1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 9.2 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 : Oligomeric assembly of Sec13-31
Entire | Name: Oligomeric assembly of Sec13-31 |
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Components |
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-Supramolecule #1000: Oligomeric assembly of Sec13-31
Supramolecule | Name: Oligomeric assembly of Sec13-31 / type: sample / ID: 1000 / Oligomeric state: 24-mer made by Interlocked Cuboctahedrons / Number unique components: 2 |
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Molecular weight | Theoretical: 8.1 MDa |
-Macromolecule #1: SEC13R
Macromolecule | Name: SEC13R / type: protein_or_peptide / ID: 1 / Name.synonym: Sec13 / Number of copies: 12 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: Sf9 |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | GO: intracellular protein transport / InterPro: WD40 repeat |
-Macromolecule #2: SEC31L1
Macromolecule | Name: SEC31L1 / type: protein_or_peptide / ID: 2 / Name.synonym: Sec31 / Number of copies: 12 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: Sf9 |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | GO: intracellular protein transport / InterPro: WD40 repeat |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
-Sample preparation
Buffer | pH: 7.5 Details: 20 mM Tris-Cl, pH 7.5, 700 mM KOAc, 1mM MgOAc, 10mM DTT |
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Grid | Details: Quantifoil 2/2, 400 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: OTHER Details: Vitrification instrument: FEI Vitrobot. Grid plasma cleaned for 5s with Gatan Solarus 950 plasma cleaner using a ratio of 75-25 of Argon and Oxygen respectively. Method: Temperature of chamber was 4 degrees C. 0 seconds drain time. Single blot. 0 mm offset. 3 ul sample applied to grid. Blot for 2.5 seconds before plunging. |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 64 |
Electron beam | Acceleration voltage: 300 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 24000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 64 ° / Tilt series - Axis1 - Angle increment: 2 ° |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 85.0 Å / Resolution method: OTHER / Software - Name: PROTOMO / Number images used: 250 |
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CTF correction | Details: Phase correction for each image |