+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1232 | |||||||||
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Title | Structure of the Sec13-31 COPII coat cage. | |||||||||
Map data | This is a 30 angstrom resolution map of the self-assembing Sec13/31 cage. | |||||||||
Sample |
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Function / homology | COPII vesicle coat / intracellular protein transport / WD40 repeat Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 30.0 Å | |||||||||
Authors | Stagg SM / Gurkan C / Fowler DM / LaPointe P / Foss TR / Potter CS / Carragher B / Balch WE | |||||||||
Citation | Journal: Nature / Year: 2006 Title: Structure of the Sec13/31 COPII coat cage. Authors: Scott M Stagg / Cemal Gürkan / Douglas M Fowler / Paul LaPointe / Ted R Foss / Clinton S Potter / Bridget Carragher / William E Balch / Abstract: Endomembranes of eukaryotic cells are dynamic structures that are in continuous communication through the activity of specialized cellular machineries, such as the coat protein complex II (COPII), ...Endomembranes of eukaryotic cells are dynamic structures that are in continuous communication through the activity of specialized cellular machineries, such as the coat protein complex II (COPII), which mediates cargo export from the endoplasmic reticulum (ER). COPII consists of the Sar1 GTPase, Sec23 and Sec24 (Sec23/24), where Sec23 is a Sar1-specific GTPase-activating protein and Sec24 functions in cargo selection, and Sec13 and Sec31 (Sec13/31), which has a structural role. Whereas recent results have shown that Sec23/24 and Sec13/31 can self-assemble to form COPII cage-like particles, we now show that Sec13/31 can self-assemble to form minimal cages in the absence of Sec23/24. We present a three-dimensional reconstruction of these Sec13/31 cages at 30 A resolution using cryo-electron microscopy and single particle analysis. These results reveal a novel cuboctahedron geometry with the potential to form a flexible lattice and to generate a diverse range of containers. Our data are consistent with a model for COPII coat complex assembly in which Sec23/24 has a non-structural role as a multivalent ligand localizing the self-assembly of Sec13/31 to form a cage lattice driving ER cargo export. | |||||||||
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_1232.map.gz | 21 MB | EMDB map data format | |
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Header (meta data) | emd-1232-v30.xml emd-1232.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | 1232.gif EMD-1232.png | 13.2 KB 137.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1232 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1232 | 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_1232.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a 30 angstrom resolution map of the self-assembing Sec13/31 cage. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.526 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 of Sec13-31 heterotetramers forming a cuboctahedron Number unique components: 2 |
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Molecular weight | Theoretical: 8.14 MDa |
-Macromolecule #1: Sec13
Macromolecule | Name: Sec13 / type: protein_or_peptide / ID: 1 / Name.synonym: Sec13 / Details: SEC13R / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 33 MDa / Theoretical: 33 MDa |
Recombinant expression | Organism: Baculovirus infected Tn5 insect cells / Recombinant plasmid: pFastBac |
Sequence | GO: intracellular protein transport / InterPro: WD40 repeat |
-Macromolecule #2: Sec31
Macromolecule | Name: Sec31 / type: protein_or_peptide / ID: 2 / Name.synonym: Sec31 / Details: SEC31L1 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 139 MDa / Theoretical: 139 MDa |
Recombinant expression | Organism: Baculovirus infected Tn5 insect cells / Recombinant plasmid: pFastBac |
Sequence | GO: COPII vesicle coat / InterPro: WD40 repeat |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 6.5 / Details: 50mM MES pH 6.5, 225mM KOAc, 1mM MgCl2 |
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 30s with Fischione 1020 plasma cleaner using 75-25 Argon-Oxygen mix. Method: Temperature of chamber was 4 degrees C. 0 seconds drain time. Single blot. 0 mm offset. 4 ul sample applied to grid. Blot for 3.0 seconds before plunging. |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder. Specimen holder model: GATAN LIQUID NITROGEN |
Temperature | Average: 94 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 50,000X magnification |
Date | Feb 2, 2005 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
-Image processing
CTF correction | Details: Phase correction for each particle. |
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Final two d classification | Number classes: 92 |
Final reconstruction | Applied symmetry - Point group: O (octahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 9777 |
Details | The images were acquired using the Leginon automated data aquisition system. The particles were automatically selected using the Selexon package. The CTF was automatically estimated using the ACE package |