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Yorodumi- PDB-7ozr: Subtomogram average of authentic mumps virus nucleocapsid from He... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ozr | ||||||
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Title | Subtomogram average of authentic mumps virus nucleocapsid from HeLa cell lysate of long helical pitch | ||||||
Components |
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Keywords | VIRUS / Helical filament / Nucleocapsid / Protein-RNA complex / Scaffold | ||||||
Function / homology | Function and homology information helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding Similarity search - Function | ||||||
Biological species | Mumps virus genotype A | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Mahamid, J. / Zhang, X. | ||||||
Funding support | European Union, 1items
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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, C.E. / Ching, C. / Pflaesterer, T. / Fung, H.K.H. / Poser, I. / Mueller, C.W. / Hyman, A.A. / Savitski, M.M. / Mahamid, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ozr.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ozr.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ozr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ozr_validation.pdf.gz | 882.3 KB | Display | wwPDB validaton report |
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Full document | 7ozr_full_validation.pdf.gz | 889.9 KB | Display | |
Data in XML | 7ozr_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 7ozr_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/7ozr ftp://data.pdbj.org/pub/pdb/validation_reports/oz/7ozr | HTTPS FTP |
-Related structure data
Related structure data | 13133MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 61316.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mumps virus genotype A / References: UniProt: A0A2Z4K4B8 |
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#2: RNA chain | Mass: 1792.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mumps virus genotype A |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Authentic Mumps virus nucleocapsid-RNA complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Mumps virus genotype A |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: homo sap |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.6 sec. / Electron dose: 2.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 8 / Used frames/image: 1-8 |
-Processing
Software | Name: PHENIX / Version: 1.18_3845: / Classification: refinement | |||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -27.17 ° / Axial rise/subunit: 4.21 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 939 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||
EM volume selection | Method: filament tracing / Num. of tomograms: 20 / Num. of volumes extracted: 939 | |||||||||||||||||||||||||||||||||
Atomic model building | B value: 56.3 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | |||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4XJN Pdb chain-ID: A / Accession code: 4XJN / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.36 Å2 | |||||||||||||||||||||||||||||||||
Refine LS restraints |
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