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Structures from COPI-coated vesicles: triad
by subtomogram averaging, at 26 A resolution
#1: Surface view with section colored by density value, Surface level: 0.537, Made by UCSF CHIMERA
#2: Surface view colored by height, Surface level: 0.537, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 2084 |
|---|---|
| Title | Structures from COPI-coated vesicles: triad |
| Map | Reconstruction of a triad |
| Sample | triad |
| Keywords |  COPI-coated vesicles, subtomogram averaging, membrane trafficking, protein coat, coatomer, COPI |
| Authors | Faini M, Prinz S, Beck R, Schorb M, Riches JD, Bacia K, Brugger B, Wieland FT, Briggs JAG |
| Date | Deposition: 2012-04-20, Header release: 2012-05-24, Map release: 2012-05-25, Last update: 2012-08-29 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.537, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 0.537, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Science, Vol. 336, Issue 6087, Page 1451-4, Year 2012 |
|---|---|
| Title | The structures of COPI-coated vesicles reveal alternate coatomer conformations and interactions. |
| Authors | Marco Faini, Simone Prinz, Rainer Beck, Martin Schorb, James D Riches, Kirsten Bacia, Britta Brügger, Felix T Wieland, John A G Briggs Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. |
| Keywords | Animals, COP-Coated Vesicles (chemistry), Coat Protein Complex I (chemistry), Coatomer Protein (chemistry), Cryoelectron Microscopy, Electron Microscope Tomography, Image Processing, Computer-Assisted, Mice, Models, Molecular, Protein Conformation |
| Links | DOI: 10.1126/science.1221443, PubMed: 22628556 |
 Map | |||||||||||||||||||||||||
| File |  EMD-2084.map ( map file in CCP4 format, 5621 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 553.28 A , B = 553.28 A , C = 553.28 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 4.94 A , Y = 4.94 A , Z = 4.94 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Reconstruction of a triad | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | triad |
|---|---|
| Number of Components | 3 |
| Component #1: cellular-component - liposome membrane | |
| Scientific name | liposome membrane |
| Scientific Name of Species | unidentified (NCBI Taxonomy: 32644) |
| Recombinant expression | No |
| Component #2: protein - COPI | |
| Scientific name | Coatomer complex |
| Common Name | COPI |
| Theoretical Mass | 0.560 MDa |
| Number of Copies | 3 |
| Scientific Name of Species | Mus musculus (NCBI Taxonomy: 10090)
|
| Common Name of Species | Mouse |
| Recombinant expression | Yes |
| Engineered Source | Exp System: unidentified baculovirus (NCBI Taxonomy: 10469) |
| Component #3: protein - Arf1 | |
| Scientific name | Arf1 |
| Theoretical Mass | 0.020 MDa |
| Scientific Name of Species | Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
|
| Common Name of Species | Baker's Yeast |
| Recombinant expression | Yes |
| Engineered Source | Exp System: Escherichia coli (NCBI Taxonomy: 562) |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | 300 mesh copper grid with holey carbon support, glow discharged |
|---|---|
| Buffer | Details: 50mM Hepes , 50 mM KOAc, 1 mM MgCl2 pH: 7.5 |
| Vitrification | |
| Method | Hand plunging |
| Cryogen Name | ETHANE |
| Humidity | 100 |
| Instrument | OTHER |
| Temperature | 90 Kelvin |
| Imaging | |
| Microscope | FEI POLARA 300 |
| Date | 06-MAY-2011 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 60 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 27500 X, |
| Nominal Cs | 2.0 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 2300 nm - 4300 nm |
| Energy Filter | Type: Gatan GIF 2000 , Window: |
| Specimen Holder | |
| Holder | ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | -60 degrees - 60 degrees |
| Temperature | ( 90 Kelvin - ) |
| Camera | |
| Detector | CCD Camera |
| Image Acquisition | |
| Quant Bit Number | 14 |
 Processing | |
| Method | subtomogram averaging |
|---|---|
| 3 D reconstruction | |
| Algorithm | Subtomogram averaging |
| Software | IMOD, TOM, package, Matlab |
| CTF Correction | CTF multiplication |
| Resolution By Author | 26 |
| Resolution Method | FSC at 0.5 cut-off, independently processed datasets |
| Subtomogram Averaging | |
| Details | CTF correction was performed. Average number of tilts used in the 3D reconstructions: 41. Average tomographic tilt angle increment: 3. |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-2084.xml (8.2 KB) | ||
|---|---|---|---|
| Map data | emd_2084.map.gz (3.8 MB) | ||
| Images | emd_2084.tif (176.9 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2084 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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