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Yorodumi- EMDB-13167: Mumps viral factory at a chronic infection stage in a HeLa cell u... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13167 | |||||||||
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Title | Mumps viral factory at a chronic infection stage in a HeLa cell under prolonged mild arsenite stress | |||||||||
Map data | Tomogram of a viral factory in HeLa cells chronically infected by mumps virus after 6 h of 30 uM arsenite stress | |||||||||
Sample |
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Keywords | Cryo-ET / cryo-FIB / Helical filament / Nucleocapsid / Protein-RNA complex / Viral factories / Host-virus / VIRUS | |||||||||
Biological species | Mumps virus genotype A | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Mahamid J / Zhang X / Ching C | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Cell / Year: 2023 Title: Molecular mechanisms of stress-induced reactivation in mumps virus condensates. Authors: Xiaojie Zhang / Sindhuja Sridharan / Ievgeniia Zagoriy / Christina Eugster Oegema / Cyan Ching / Tim Pflaesterer / Herman K H Fung / Isabelle Becher / Ina Poser / Christoph W Müller / ...Authors: Xiaojie Zhang / Sindhuja Sridharan / Ievgeniia Zagoriy / Christina Eugster Oegema / Cyan Ching / Tim Pflaesterer / Herman K H Fung / Isabelle Becher / Ina Poser / Christoph W Müller / Anthony A Hyman / Mikhail M Savitski / Julia Mahamid / Abstract: Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions in the human host and cause chronic diseases. Here, we uncover how cellular ...Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions in the human host and cause chronic diseases. Here, we uncover how cellular stress disrupts the metastable host-virus equilibrium in persistent infection and induces viral replication in a culture model of mumps virus. Using a combination of cell biology, whole-cell proteomics, and cryo-electron tomography, we show that persistent viral replication factories are dynamic condensates and identify the largely disordered viral phosphoprotein as a driver of their assembly. Upon stress, increased phosphorylation of the phosphoprotein at its interaction interface with the viral polymerase coincides with the formation of a stable replication complex. By obtaining atomic models for the authentic mumps virus nucleocapsid, we elucidate a concomitant conformational change that exposes the viral genome to its replication machinery. These events constitute a stress-mediated switch within viral condensates that provide an environment to support upregulation of viral replication. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13167.map.gz | 488 MB | EMDB map data format | |
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Header (meta data) | emd-13167-v30.xml emd-13167.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_13167.png | 286.6 KB | ||
Masks | emd_13167_msk_1.map | 527.3 MB | Mask map | |
Filedesc metadata | emd-13167.cif.gz | 4.2 KB | ||
Others | emd_13167_additional_1.map.gz | 10.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13167 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13167 | HTTPS FTP |
-Validation report
Summary document | emd_13167_validation.pdf.gz | 563.9 KB | Display | EMDB validaton report |
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Full document | emd_13167_full_validation.pdf.gz | 563.5 KB | Display | |
Data in XML | emd_13167_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | emd_13167_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13167 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13167 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13167.map.gz / Format: CCP4 / Size: 527.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Tomogram of a viral factory in HeLa cells chronically infected by mumps virus after 6 h of 30 uM arsenite stress | ||||||||||||||||||||
Voxel size | X=Y=Z: 13.048 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_13167_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Tomogram and nucleocapsid tracing of a viral factory...
File | emd_13167_additional_1.map | ||||||||||||
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Annotation | Tomogram and nucleocapsid tracing of a viral factory in HeLa cells chronically infected by mumps virus after 6 h of 30 uM arsenite stress | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cytoplasmic mumps viral factory at chronic infection stage in a H...
Entire | Name: Cytoplasmic mumps viral factory at chronic infection stage in a HeLa cell after 6 h of 30 uM arsenite stress |
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Components |
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-Supramolecule #1: Cytoplasmic mumps viral factory at chronic infection stage in a H...
Supramolecule | Name: Cytoplasmic mumps viral factory at chronic infection stage in a HeLa cell after 6 h of 30 uM arsenite stress type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mumps virus genotype A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 120 Focused ion beam - Details: Rough milling was done with currents of 1 nA, gradually reduced to lower currents, down to 50 pA for the final polishing step. The value given for _em_focused_ion_beam. ...Focused ion beam - Details: Rough milling was done with currents of 1 nA, gradually reduced to lower currents, down to 50 pA for the final polishing step. The value given for _em_focused_ion_beam.instrument is Aquilos Cryo-FIB. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Digitization - Frames/image: 1-11 / Number real images: 61 / Average exposure time: 0.14 sec. / Average electron dose: 2.61 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 min: 3.0 µm / Nominal magnification: 53000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / 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: 45 |
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