+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1511 | |||||||||
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Title | COPII coat | |||||||||
Map data | This is a reconstruction of a COPII coat comprised of Sec13-31 and Sec23-24. | |||||||||
Sample |
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Keywords | vesicle trafficking / COPII / icosidodecahedron / secretory pathway / endoplasmic reticulum / automation | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 43.0 Å | |||||||||
Authors | Stagg SM / LaPointe P / Razvi A / Gurkan C / Potter CS / Carragher B / Balch WE | |||||||||
Citation | Journal: Cell / Year: 2008 Title: Structural basis for cargo regulation of COPII coat assembly. Authors: Scott M Stagg / Paul LaPointe / Abbas Razvi / Cemal Gürkan / Clinton S Potter / Bridget Carragher / William E Balch / Abstract: Using cryo-electron microscopy, we have solved the structure of an icosidodecahedral COPII coat involved in cargo export from the endoplasmic reticulum (ER) coassembled from purified cargo adaptor ...Using cryo-electron microscopy, we have solved the structure of an icosidodecahedral COPII coat involved in cargo export from the endoplasmic reticulum (ER) coassembled from purified cargo adaptor Sec23-24 and Sec13-31 lattice-forming complexes. The coat structure shows a tetrameric assembly of the Sec23-24 adaptor layer that is well positioned beneath the vertices and edges of the Sec13-31 lattice. Fitting the known crystal structures of the COPII proteins into the density map reveals a flexible hinge region stemming from interactions between WD40 beta-propeller domains present in Sec13 and Sec31 at the vertices. The structure shows that the hinge region can direct geometric cage expansion to accommodate a wide range of bulky cargo, including procollagen and chylomicrons, that is sensitive to adaptor function in inherited disease. The COPII coat structure leads us to propose a mechanism by which cargo drives cage assembly and membrane curvature for budding from the ER. | |||||||||
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_1511.map.gz | 13.7 MB | EMDB map data format | |
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Header (meta data) | emd-1511-v30.xml emd-1511.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | 1511.gif | 48.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1511 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1511 | 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_1511.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 reconstruction of a COPII coat comprised of Sec13-31 and Sec23-24. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.7 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 : Sec13/31 bound to Sec23/24
Entire | Name: Sec13/31 bound to Sec23/24 |
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Components |
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-Supramolecule #1000: Sec13/31 bound to Sec23/24
Supramolecule | Name: Sec13/31 bound to Sec23/24 / type: sample / ID: 1000 Oligomeric state: 60 Sec13-31 heterotetramers bound to 120 Sec23-24 heterodimers Number unique components: 4 |
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Molecular weight | Theoretical: 44.8 MDa |
-Supramolecule #1: COPII coat
Supramolecule | Name: COPII coat / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Sec13-31 and Sec23-24 / Recombinant expression: Yes |
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Ref GO | 0: GO:0006888 |
Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: cytosol |
Molecular weight | Experimental: 44.8 MDa / Theoretical: 44.8 MDa |
Recombinant expression | Organism: Insect cells / Recombinant plasmid: bacmid |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 Details: 50 mM MES pH 6.8, 700 mM KOAc, 1 mM MgOAc, 1 mM DTT |
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Grid | Details: 400 mesh grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 98 K / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: blot for 3 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 88 K |
Alignment procedure | Legacy - Astigmatism: astigmatism corrected automatically with Leginon. |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 29000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus min: 10.0 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Data was automatically collected using Leginon. Data was processed automatically with Appion. Particles were picked manually. |
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CTF correction | Details: each particle |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 43.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Details: Final map was lowpass filtered to 43 angstroms / Number images used: 12120 |
Final two d classification | Number classes: 212 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Normal mode-based flexible fitting (nmff) and chimera |
Details | Protocol: normal modes flexible fitting and rigid body. A bend was modeled into Sec13-31 using the program nmff. Sec13-31 and Sec23-24 were separately fitted into the cryoEM density using the program Chimera. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: nmff and chimera |
Details | Protocol: normal modes flexible fitting and rigid body. A bend was modeled into Sec13-31 using the program nmff. Sec13-31 and Sec23-24 were separately fitted into the cryoEM density using the program Chimera. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
-Atomic model buiding 3
Initial model | PDB ID: |
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Software | Name: nmff and chimera |
Details | Protocol: normal modes flexible fitting and rigid body. A bend was modeled into Sec13-31 using the program nmff. Sec13-31 and Sec23-24 were separately fitted into the cryoEM density using the program Chimera. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |