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Yorodumi- EMDB-16301: Subtomogram average of double-stranded RNA of chikungunya virus s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16301 | ||||||||||||
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Title | Subtomogram average of double-stranded RNA of chikungunya virus spherules, class 4 | ||||||||||||
Map data | Subtomogram average of double-stranded RNA of chikungunya virus spherules, class 4 | ||||||||||||
Sample |
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Keywords | virus / alphavirus / chikungunya / RNA | ||||||||||||
Biological species | Chikungunya virus | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 71.0 Å | ||||||||||||
Authors | Laurent T / Carlson LA | ||||||||||||
Funding support | France, Sweden, 3 items
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Citation | Journal: PLoS Negl Trop Dis / Year: 2023 Title: The organization of double-stranded RNA in the chikungunya virus replication organelle. Authors: Timothée Laurent / Lars-Anders Carlson / Abstract: Alphaviruses are mosquito-borne, positive-sense single-stranded RNA viruses. Amongst the alphaviruses, chikungunya virus is notable as a large source of human illness, especially in tropical and ...Alphaviruses are mosquito-borne, positive-sense single-stranded RNA viruses. Amongst the alphaviruses, chikungunya virus is notable as a large source of human illness, especially in tropical and subtropical regions. When they invade a cell, alphaviruses generate dedicated organelles for viral genome replication, so-called spherules. Spherules form as outward-facing buds at the plasma membrane, and it has recently been shown that the thin membrane neck that connects this membrane bud with the cytoplasm is guarded by a two-megadalton protein complex that contains all the enzymatic functions necessary for RNA replication. The lumen of the spherules contains a single copy of the negative-strand template RNA, present in a duplex with newly synthesized positive-sense RNA. Less is known about the organization of this double-stranded RNA as compared to the protein components of the spherule. Here, we analyzed cryo-electron tomograms of chikungunya virus spherules in terms of the organization of the double-stranded RNA replication intermediate. We find that the double-stranded RNA has a shortened apparent persistence length as compared to unconstrained double-stranded RNA. Around half of the genome is present in either of five conformations identified by subtomogram classification, each representing a relatively straight segment of ~25-32 nm. Finally, the RNA occupies the spherule lumen at a homogeneous density, but has a preferred orientation to be perpendicular to a vector pointing from the membrane neck towards the spherule center. Taken together, this analysis lays another piece of the puzzle of the highly coordinated alphavirus genome replication. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16301.map.gz | 454.5 KB | EMDB map data format | |
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Header (meta data) | emd-16301-v30.xml emd-16301.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_16301.png | 7.6 KB | ||
Others | emd_16301_half_map_1.map.gz emd_16301_half_map_2.map.gz | 453.7 KB 453.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16301 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16301 | HTTPS FTP |
-Validation report
Summary document | emd_16301_validation.pdf.gz | 707.7 KB | Display | EMDB validaton report |
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Full document | emd_16301_full_validation.pdf.gz | 707.2 KB | Display | |
Data in XML | emd_16301_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_16301_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16301 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16301 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16301.map.gz / Format: CCP4 / Size: 489.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Subtomogram average of double-stranded RNA of chikungunya virus spherules, class 4 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.58 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map
File | emd_16301_half_map_1.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_16301_half_map_2.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : dsRNA of chikungunya spherule
Entire | Name: dsRNA of chikungunya spherule |
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Components |
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-Supramolecule #1: dsRNA of chikungunya spherule
Supramolecule | Name: dsRNA of chikungunya spherule / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Chikungunya virus |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 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: 5.0 µm / Nominal defocus min: 3.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 71.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 135 |
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Extraction | Number tomograms: 2 / Number images used: 905 |
Final 3D classification | Number classes: 5 / Avg.num./class: 150 / Software - Name: Dynamo |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: Dynamo |