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Yorodumi- EMDB-13137: In-cell subtomogram average of authentic mumps virus nucleocapsid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13137 | |||||||||
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Title | In-cell subtomogram average of authentic mumps virus nucleocapsid in HeLa cells | |||||||||
Map data | Authentic mumps virus nucleocapsid inside HeLa cells at prolonged stress treatment by subtomogram averaging | |||||||||
Sample |
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Keywords | Helical filament / Nucleocapsid / Protein-RNA complex / Scaffold / VIRUS | |||||||||
Biological species | Mumps virus genotype A | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 6.5 Å | |||||||||
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_13137.map.gz | 8.1 MB | EMDB map data format | |
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Header (meta data) | emd-13137-v30.xml emd-13137.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13137_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_13137.png | 44 KB | ||
Filedesc metadata | emd-13137.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13137 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13137 | HTTPS FTP |
-Validation report
Summary document | emd_13137_validation.pdf.gz | 460.7 KB | Display | EMDB validaton report |
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Full document | emd_13137_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | emd_13137_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_13137_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13137 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13137 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13137.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Authentic mumps virus nucleocapsid inside HeLa cells at prolonged stress treatment by subtomogram averaging | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.631 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Authentic Mumps virus nucleocapsid-RNA complex inside HeLa cells
Entire | Name: Authentic Mumps virus nucleocapsid-RNA complex inside HeLa cells |
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Components |
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-Supramolecule #1: Authentic Mumps virus nucleocapsid-RNA complex inside HeLa cells
Supramolecule | Name: Authentic Mumps virus nucleocapsid-RNA complex inside HeLa cells type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mumps virus genotype A |
-Macromolecule #1: Mumps virus nucleocapsid protein
Macromolecule | Name: Mumps virus nucleocapsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mumps virus genotype A |
Sequence | String: MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIRL ADRSPEAQIE RCEIDGFEPG TYRLIPNARA NLTANEIAAY ALLADDLPPT INNGTPYVHA DVEGQPCDEI EQFLDRCYSV ...String: MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIRL ADRSPEAQIE RCEIDGFEPG TYRLIPNARA NLTANEIAAY ALLADDLPPT INNGTPYVHA DVEGQPCDEI EQFLDRCYSV LIQAWVMVCK CMTAYDQPAG SADRRFAKYQ QQGRLEARYM LQPEAQRLIQ TAIRKSLVVR QYLTFELQLA RRQGLLSNRY YAMVGDIGKY IENSGLTAFF LTLKYALGTK WSPLSLAAFT GELTKLRSLM MLYRDIGEQA RYLALLEAPQ IMDFAPGGYP LIFSYAMGVG TVLDAQMRNY TYARPFLNGY YFQIGVETAR RQQGTVDNRV ADDLGLTPEQ RTEVTQLVDR LARGRGAGIP GGPVNPFVPP VQQQQPAAVY ADIPALEESD DDGDEDGGAG FQNGVQVPAV RQGGQTDFRA QPLQDPIQAQ LFMPLYPQVS NIPSNQNHQI NRIGGLENQD LLRYNENGDS QQDARGEHGN TFPNNPNQNA QLQVGDWDE |
-Macromolecule #2: RNA
Macromolecule | Name: RNA / type: rna / ID: 2 |
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Source (natural) | Organism: Mumps virus genotype A |
Sequence | String: UUUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil / Material: GOLD / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
Details | HeLa cells were chronically infected by mumps virus. HeLa cells thinned by cryo-focused ion beam milling. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 / Average exposure time: 0.16 sec. / Average electron dose: 2.6 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: 3.25 µm / Nominal defocus min: 1.75 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 |