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Yorodumi- EMDB-8748: Cryo-EM reconstruction of the Cafeteria roenbergensis virus capsi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8748 | |||||||||
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Title | Cryo-EM reconstruction of the Cafeteria roenbergensis virus capsid suggests a novel assembly pathway for giant viruses | |||||||||
Map data | Cryo-EM reconstruction of Cafeteria roenbergensis virus with icosahedral averaging | |||||||||
Sample |
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Biological species | Cafeteria roenbergensis virus BV-PW1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 21.0 Å | |||||||||
Authors | Xiao C / Fischer MG / Bolotaulo DM / Ulloa-Rondeau N / Avila GA / Suttle CA | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Cryo-EM reconstruction of the Cafeteria roenbergensis virus capsid suggests novel assembly pathway for giant viruses. Authors: Chuan Xiao / Matthias G Fischer / Duer M Bolotaulo / Nancy Ulloa-Rondeau / Gustavo A Avila / Curtis A Suttle / Abstract: Whereas the protein composition and overall shape of several giant virus capsids have been described, the mechanism by which these large capsids assemble remains enigmatic. Here, we present a ...Whereas the protein composition and overall shape of several giant virus capsids have been described, the mechanism by which these large capsids assemble remains enigmatic. Here, we present a reconstruction of the capsid of Cafeteria roenbergensis virus (CroV), one of the largest viruses analyzed by cryo-electron microscopy (cryo-EM) to date. The CroV capsid has a diameter of 3,000 Å and a Triangulation number of 499. Unlike related mimiviruses, the CroV capsid is not decorated with glycosylated surface fibers, but features 30 Å-long surface protrusions that are formed by loops of the major capsid protein. Based on the orientation of capsomers in the cryo-EM reconstruction, we propose that the capsids of CroV and related giant viruses are assembled by a newly conceived assembly pathway that initiates at a five-fold vertex and continuously proceeds outwards in a spiraling fashion. | |||||||||
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_8748.map.gz | 455.4 MB | EMDB map data format | |
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Header (meta data) | emd-8748-v30.xml emd-8748.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8748_fsc.xml | 21.3 KB | Display | FSC data file |
Images | emd_8748.png | 329.2 KB | ||
Masks | emd_8748_msk_1.map emd_8748_msk_2.map | 524.1 MB 524.1 MB | Mask map | |
Others | emd_8748_half_map_1.map.gz emd_8748_half_map_2.map.gz | 299.8 MB 299.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8748 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8748 | HTTPS FTP |
-Validation report
Summary document | emd_8748_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_8748_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_8748_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8748 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8748 | 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_8748.map.gz / Format: CCP4 / Size: 524.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of Cafeteria roenbergensis virus with icosahedral averaging | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.156 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_8748_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_8748_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Even map without soft masking of the reconstruction...
File | emd_8748_half_map_1.map | ||||||||||||
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Annotation | Even map without soft masking of the reconstruction of Cafeteria roenbergensis virus with icosahedral averaging | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Odd map without soft masking of the reconstruction...
File | emd_8748_half_map_2.map | ||||||||||||
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Annotation | Odd map without soft masking of the reconstruction of Cafeteria roenbergensis virus with icosahedral averaging | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cafeteria roenbergensis virus BV-PW1
Entire | Name: Cafeteria roenbergensis virus BV-PW1 |
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Components |
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-Supramolecule #1: Cafeteria roenbergensis virus BV-PW1
Supramolecule | Name: Cafeteria roenbergensis virus BV-PW1 / type: virus / ID: 1 / Parent: 0 Details: The virus was purified following the protocol described in Fischer, M.G., et. al. The virion of Cafeteria roenbergensis virus (CroV) contains a complex suite of proteins for transcription ...Details: The virus was purified following the protocol described in Fischer, M.G., et. al. The virion of Cafeteria roenbergensis virus (CroV) contains a complex suite of proteins for transcription and DNA repair - Virology 466-467, 82-94 (2014). NCBI-ID: 693272 / Sci species name: Cafeteria roenbergensis virus BV-PW1 / Sci species strain: BV-PW1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Cafeteria roenbergensis (eukaryote) |
Virus shell | Shell ID: 1 / Name: CroV / Diameter: 3000.0 Å / T number (triangulation number): 499 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Grid | Model: Quantifoil S7/2 / Material: COPPER |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/ST |
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Image recording | Film or detector model: KODAK SO-163 FILM / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |