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Yorodumi- PDB-8usn: Intracellular cryo-tomography structure of EBOV nucleocapsid at 8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8usn | ||||||
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Title | Intracellular cryo-tomography structure of EBOV nucleocapsid at 8.9 Angstrom | ||||||
Components |
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Keywords | VIRAL PROTEIN / nucleoprotein / nucleocapsid / Ebola virus / EBOV / filovirus / subtomogram averaging / cryo-ET / FIB / intracellular / in situ | ||||||
Function / homology | Function and homology information suppression by virus of host intracellular interferon activity / suppression by virus of host cytokine production / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II ...suppression by virus of host intracellular interferon activity / suppression by virus of host cytokine production / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation / viral RNA genome packaging / molecular sequestering activity / helical viral capsid / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral genome replication / viral budding from plasma membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / negative regulation of gene expression / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / membrane Similarity search - Function | ||||||
Biological species | Ebola virus - Mayinga Zaire (virus) 1976 | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8.9 Å | ||||||
Authors | Watanabe, R. / Zyla, D. / Saphire, E.O. | ||||||
Funding support | 1items
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Citation | Journal: Cell / Year: 2024 Title: Intracellular Ebola virus nucleocapsid assembly revealed by in situ cryo-electron tomography. Authors: Reika Watanabe / Dawid Zyla / Diptiben Parekh / Connor Hong / Ying Jones / Sharon L Schendel / William Wan / Guillaume Castillon / Erica Ollmann Saphire / Abstract: Filoviruses, including the Ebola and Marburg viruses, cause hemorrhagic fevers with up to 90% lethality. The viral nucleocapsid is assembled by polymerization of the nucleoprotein (NP) along the ...Filoviruses, including the Ebola and Marburg viruses, cause hemorrhagic fevers with up to 90% lethality. The viral nucleocapsid is assembled by polymerization of the nucleoprotein (NP) along the viral genome, together with the viral proteins VP24 and VP35. We employed cryo-electron tomography of cells transfected with viral proteins and infected with model Ebola virus to illuminate assembly intermediates, as well as a 9 Å map of the complete intracellular assembly. This structure reveals a previously unresolved third and outer layer of NP complexed with VP35. The intrinsically disordered region, together with the C-terminal domain of this outer layer of NP, provides the constant width between intracellular nucleocapsid bundles and likely functions as a flexible tether to the viral matrix protein in the virion. A comparison of intracellular nucleocapsids with prior in-virion nucleocapsid structures reveals that the nucleocapsid further condenses vertically in the virion. The interfaces responsible for nucleocapsid assembly are highly conserved and offer targets for broadly effective antivirals. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8usn.cif.gz | 252.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8usn.ent.gz | 150.7 KB | Display | PDB format |
PDBx/mmJSON format | 8usn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8usn_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8usn_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8usn_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 8usn_validation.cif.gz | 69.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/8usn ftp://data.pdbj.org/pub/pdb/validation_reports/us/8usn | HTTPS FTP |
-Related structure data
Related structure data | 42509MC 8ustC 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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-Components
#1: Protein | Mass: 83387.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: The N-terminal part of nucleoprotein / Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: NP / Production host: Homo sapiens (human) / Strain (production host): HEK 293T / References: UniProt: P18272 #2: RNA chain | Mass: 1930.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sample RNA sequence / Source: (gene. exp.) Zaire (virus) / Production host: Homo sapiens (human) / Strain (production host): HEK 293T #3: Protein | Mass: 28250.811 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: VP24 / Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: VP24 / Production host: Homo sapiens (human) / Strain (production host): HEK 293T / References: UniProt: Q05322 #4: Protein | Mass: 37403.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C-terminal domain of VP35 / Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: VP35 / Production host: Homo sapiens (human) / Strain (production host): HEK 293T / References: UniProt: Q05127 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Details of virus |
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Natural host |
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Buffer solution | pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: FIB-milled-plunge-frozen cell expressing EBOV NP(601-739 truncated), VP24 and VP35 | ||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
-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 defocus max: 3500 nm / Nominal defocus min: 2500 nm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 3.5 e/Å2 / Avg electron dose per subtomogram: 160 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28000 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 25 / Num. of volumes extracted: 102000 | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT |