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Yorodumi- PDB-8arh: In situ subtomogram average of Vaccinia virus (WR) D13 lattice, o... -
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-Basic information
Entry | Database: PDB / ID: 8arh | ||||||
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Title | In situ subtomogram average of Vaccinia virus (WR) D13 lattice, on immature virions | ||||||
Components | Scaffold protein D13 | ||||||
Keywords | VIRUS / Palisade / Lattice / A4 | ||||||
Function / homology | Poxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / Scaffold protein OPG125 Function and homology information | ||||||
Biological species | Vaccinia virus WR | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 19.2 Å | ||||||
Authors | Calcraft, T. / Hernandez-Gonzalez, M. / Nans, A. / Rosenthal, P.B. / Way, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: PLoS Biol / Year: 2023 Title: A succession of two viral lattices drives vaccinia virus assembly. Authors: Miguel Hernandez-Gonzalez / Thomas Calcraft / Andrea Nans / Peter B Rosenthal / Michael Way / Abstract: During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped ...During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped intracellular mature virions (IMV) that lack D13. Here, we performed cryo-electron tomography (cryo-ET) of frozen-hydrated vaccinia-infected cells to structurally characterise the maturation process in situ. During IMV formation, a new viral core forms inside IV with a wall consisting of trimeric pillars arranged in a new pseudohexagonal lattice. This lattice appears as a palisade in cross-section. As maturation occurs, which involves a 50% reduction in particle volume, the viral membrane becomes corrugated as it adapts to the newly formed viral core in a process that does not appear to require membrane removal. Our study suggests that the length of this core is determined by the D13 lattice and that the consecutive D13 and palisade lattices control virion shape and dimensions during vaccinia assembly and maturation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8arh.cif.gz | 532 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8arh.ent.gz | 430.2 KB | Display | PDB format |
PDBx/mmJSON format | 8arh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8arh_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8arh_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8arh_validation.xml.gz | 80.1 KB | Display | |
Data in CIF | 8arh_validation.cif.gz | 127.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/8arh ftp://data.pdbj.org/pub/pdb/validation_reports/ar/8arh | HTTPS FTP |
-Related structure data
Related structure data | 15602MC 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: 61948.531 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus WR / Strain: Western Reserve / Gene: VACWR118, D13L / Cell line (production host): HeLa / Production host: Homo sapiens (human) / References: UniProt: P68440 |
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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
Component | Name: Vaccinia virus WR / Type: VIRUS / Details: A36-YdF deltaNPF1-3 deltaF11 / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Vaccinia virus WR |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HeLa |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K |
-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: 11600 X / Nominal defocus max: 8000 nm / Nominal defocus min: 8000 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.7 e/Å2 / Avg electron dose per subtomogram: 66.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 4 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 19.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34092 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 13 / Num. of volumes extracted: 341376 | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7VFE Accession code: 7VFE / Source name: PDB / Type: experimental model |