+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5408 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The Structure of the Sec13/31 COPII Cage Bound to Sec23 | |||||||||
Map data | Reconstruction of COPII coat | |||||||||
Sample |
| |||||||||
Keywords | COPII / Sec13/31 / Sec23 / secretory pathway | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 38.0 Å | |||||||||
Authors | Bhattacharya N / O'Donnell J / Stagg SM | |||||||||
Citation | Journal: J Mol Biol / Year: 2012 Title: The structure of the Sec13/31 COPII cage bound to Sec23. Authors: Nilakshee Bhattacharya / Jason O Donnell / Scott M Stagg / Abstract: Structural studies have revealed some of the organizing principles and mechanisms involved in the assembly of the COPII coat including the location of the Sec23/24 adapter layer. Previous studies, ...Structural studies have revealed some of the organizing principles and mechanisms involved in the assembly of the COPII coat including the location of the Sec23/24 adapter layer. Previous studies, however, were unable to unambiguously determine the positions of Sec23 and Sec24 in the coat. Here, we have determined a cryogenic electron microscopic structure of Sec13/31 together with Sec23. Electron tomography revealed that the binding of Sec23 induces Sec13/31 to form a variety of different geometries including a cuboctahedron, as was previously characterized for Sec13/31 alone. Single-particle reconstruction of the Sec13/31-23 cuboctahedra revealed that the binding of Sec23 induces a conformational change in Sec13/31, resulting in a more extended conformation. Docking Sec23 crystal structures into the electron microscopy map suggested that Sec24 projects its cargo binding surface out into the large open faces of the coat. These results have implications for the mechanisms by which COPII transports large cargos, cargos with large intracellular domains, and for tethering complexes that must project out of the coat in order to interact with their binding partners. Furthermore, Sec23 binds Sec13/31 at two unique sites in the coat, which suggests that each site may have unique roles in the mechanisms of COPII vesiculation. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5408.map.gz | 20.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-5408-v30.xml emd-5408.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | emd_5408.png | 55.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5408 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5408 | HTTPS FTP |
-Validation report
Summary document | emd_5408_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_5408_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_5408_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5408 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5408 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_5408.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of COPII coat | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.78 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Sec13/31-23 coat
Entire | Name: Sec13/31-23 coat |
---|---|
Components |
|
-Supramolecule #1000: Sec13/31-23 coat
Supramolecule | Name: Sec13/31-23 coat / type: sample / ID: 1000 / Oligomeric state: heterotetramer Sec13/31 binds to Sec23 / Number unique components: 3 |
---|---|
Molecular weight | Theoretical: 7.1 MDa |
-Macromolecule #1: COPII
Macromolecule | Name: COPII / type: protein_or_peptide / ID: 1 / Details: expressed in insect cells / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Homo sapiens (human) / Organelle: cytoplasm |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant plasmid: pfastBAC |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
---|---|
Buffer | pH: 7.5 Details: 700 mM potassium acetate, 25 mM HEPES, 1 mM magnesium acetate, 1mM DTT |
Staining | Type: NEGATIVE / Details: Cryo-grids |
Grid | Details: R 2/2 Quantifoil |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK I / Method: blot for 2 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Date | Sep 9, 2010 |
Image recording | Category: FILM / Film or detector model: GENERIC CCD / Digitization - Scanner: OTHER / Number real images: 2850 / Average electron dose: 30 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 37000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each image |
---|---|
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 38.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MRC,spider,coran / Number images used: 9571 |