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Yorodumi- EMDB-15583: Cryo-electron tomogram of chikungunya virus spherules at plasma m... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15583 | |||||||||||||||
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Title | Cryo-electron tomogram of chikungunya virus spherules at plasma membrane | |||||||||||||||
Map data | Cryo-electron tomogram of chikungunya virus spherules at the plasma membrane | |||||||||||||||
Sample |
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Biological species | Chikungunya virus | |||||||||||||||
Method | electron tomography / cryo EM | |||||||||||||||
Authors | Laurent T / Carlson LA | |||||||||||||||
Funding support | Sweden, France, 4 items
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Citation | Journal: Elife / Year: 2022 Title: Architecture of the chikungunya virus replication organelle. Authors: Timothée Laurent / Pravin Kumar / Susanne Liese / Farnaz Zare / Mattias Jonasson / Andreas Carlson / Lars-Anders Carlson / Abstract: are mosquito-borne viruses that cause serious disease in humans and other mammals. Along with its mosquito vector, the s chikungunya virus (CHIKV) has spread explosively in the last 20 years, and ... are mosquito-borne viruses that cause serious disease in humans and other mammals. Along with its mosquito vector, the s chikungunya virus (CHIKV) has spread explosively in the last 20 years, and there is no approved treatment for chikungunya fever. On the plasma membrane of the infected cell, CHIKV generates dedicated organelles for viral RNA replication, so-called spherules. Whereas structures exist for several viral proteins that make up the spherule, the architecture of the full organelle is unknown. Here, we use cryo-electron tomography to image CHIKV spherules in their cellular context. This reveals that the viral protein nsP1 serves as a base for the assembly of a larger protein complex at the neck of the membrane bud. Biochemical assays show that the viral helicase-protease nsP2, while having no membrane affinity on its own, is recruited to membranes by nsP1. The tomograms further reveal that full-sized spherules contain a single copy of the viral genome in double-stranded form. Finally, we present a mathematical model that explains the membrane remodeling of the spherule in terms of the pressure exerted on the membrane by the polymerizing RNA, which provides a good agreement with the experimental data. The energy released by RNA polymerization is found to be sufficient to remodel the membrane to the characteristic spherule shape. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15583.map.gz | 1.6 GB | EMDB map data format | |
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Header (meta data) | emd-15583-v30.xml emd-15583.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | emd_15583.png | 255.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15583 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15583 | HTTPS FTP |
-Validation report
Summary document | emd_15583_validation.pdf.gz | 476.1 KB | Display | EMDB validaton report |
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Full document | emd_15583_full_validation.pdf.gz | 475.6 KB | Display | |
Data in XML | emd_15583_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_15583_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15583 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15583 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15583.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-electron tomogram of chikungunya virus spherules at the plasma membrane | ||||||||||||||||||||
Voxel size | X=Y=Z: 17.16 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : BHK cell transduced with chikungunya viral replicon particles
Entire | Name: BHK cell transduced with chikungunya viral replicon particles |
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Components |
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-Supramolecule #1: BHK cell transduced with chikungunya viral replicon particles
Supramolecule | Name: BHK cell transduced with chikungunya viral replicon particles type: cell / 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 | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE-PROPANE |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: CMC-Utrecht / Diameter: 5 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 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: 3.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 61 |
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CTF correction | Software: (Name: CTFFIND (ver. 4), CTFPHASEFLIP) |