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Yorodumi- EMDB-13133: Subtomogram average of authentic mumps virus nucleocapsid from He... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13133 | |||||||||
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Title | Subtomogram average of authentic mumps virus nucleocapsid from HeLa cell lysate of long helical pitch | |||||||||
Map data | Major conformation of authentic mumps virus nucleocapsid from the lysate of HeLa cells after stress treatment by subtomogram averaging | |||||||||
Sample |
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Keywords | Helical filament / Nucleocapsid / Protein-RNA complex / Scaffold / VIRUS | |||||||||
Function / homology | Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding / Nucleocapsid Function and homology information | |||||||||
Biological species | Mumps virus genotype A | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Mahamid J / Zhang X / Pflaesterer T | |||||||||
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. #1: Journal: Biorxiv / Year: 2021 Title: Condensate-mediated reactivation of mumps virus infection under stress Authors: Zhang X / Sridharan S / Zagoriy I / Oegema CE / Ching C / Pflaesterer T / Fung HKH / Poser I / Mueller CW / Hyman AA / Savitski MM / Mahamid J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13133.map.gz | 8.6 MB | EMDB map data format | |
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Header (meta data) | emd-13133-v30.xml emd-13133.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13133_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_13133.png | 41.5 KB | ||
Filedesc metadata | emd-13133.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13133 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13133 | HTTPS FTP |
-Validation report
Summary document | emd_13133_validation.pdf.gz | 490.7 KB | Display | EMDB validaton report |
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Full document | emd_13133_full_validation.pdf.gz | 490.2 KB | Display | |
Data in XML | emd_13133_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_13133_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13133 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13133 | HTTPS FTP |
-Related structure data
Related structure data | 7ozrMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13133.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Major conformation of authentic mumps virus nucleocapsid from the lysate of HeLa cells after stress treatment by subtomogram averaging | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.6938 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
Entire | Name: Authentic Mumps virus nucleocapsid-RNA complex |
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Components |
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-Supramolecule #1: Authentic Mumps virus nucleocapsid-RNA complex
Supramolecule | Name: Authentic Mumps virus nucleocapsid-RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mumps virus genotype A |
-Macromolecule #1: Nucleocapsid
Macromolecule | Name: Nucleocapsid / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mumps virus genotype A |
Molecular weight | Theoretical: 61.316734 KDa |
Sequence | String: MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIR LADRSPEAQI ERCEIDGFEP GTYRLIPNAR ANLTANEIAA YALLADDLPP TINNGTPYVH ADVEGQPCDE I EQFLDRCY ...String: MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIR LADRSPEAQI ERCEIDGFEP GTYRLIPNAR ANLTANEIAA YALLADDLPP TINNGTPYVH ADVEGQPCDE I EQFLDRCY SVLIQAWVMV CKCMTAYDQP AGSADRRFAK YQQQGRLEAR YMLQPEAQRL IQTAIRKSLV VRQYLTFELQ LA RRQGLLS NRYYAMVGDI GKYIENSGLT AFFLTLKYAL GTKWSPLSLA AFTGELTKLR SLMMLYRDIG EQARYLALLE APQ IMDFAP GGYPLIFSYA MGVGTVLDAQ MRNYTYARPF LNGYYFQIGV ETARRQQGTV DNRVADDLGL TPEQRTEVTQ LVDR LARGR GAGIPGGPVN PFVPPVQQQQ PAAVYADIPA LEESDDDGDE DGGAGFQNGV QVPAVRQGGQ TDFRAQPLQD PIQAQ LFMP LYPQVSNIPS NQNHQINRIG GLENQDLLRY NENGDSQQDA RGEHGNTFPN NPNQNAQLQV GDWDE UniProtKB: Nucleocapsid |
-Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
Macromolecule | Name: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Mumps virus genotype A |
Molecular weight | Theoretical: 1.792037 KDa |
Sequence | String: UUUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-8 / Average exposure time: 1.6 sec. / Average electron dose: 2.5 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: 3.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 81000 |
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
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 56.3 / Target criteria: Correlation coefficient |
Output model | PDB-7ozr: |