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Yorodumi- PDB-8pe4: Capsid structure of the L-A helper virus from native viral communities -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pe4 | |||||||||||||||||||||
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Title | Capsid structure of the L-A helper virus from native viral communities | |||||||||||||||||||||
Components | Major capsid protein | |||||||||||||||||||||
Keywords | VIRUS / Capsid structure ScVLA / viral particle / wildtype / endogenous | |||||||||||||||||||||
Function / homology | Major coat protein, L-A virus / L-A virus major coat protein superfamily / L-A virus, major coat protein / viral capsid / Major capsid protein Function and homology information | |||||||||||||||||||||
Biological species | Saccharomyces cerevisiae virus L-A | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å | |||||||||||||||||||||
Authors | Schmidt, L. / Tueting, C. / Stubbs, M.T. / Kastritis, P.L. | |||||||||||||||||||||
Funding support | Germany, European Union, 6items
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Citation | Journal: Commun Biol / Year: 2024 Title: Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. Authors: Lisa Schmidt / Christian Tüting / Fotis L Kyrilis / Farzad Hamdi / Dmitry A Semchonok / Gerd Hause / Annette Meister / Christian Ihling / Milton T Stubbs / Andrea Sinz / Panagiotis L Kastritis / Abstract: The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to ...The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-π stacking, widespread across viruses and within the Totiviridae, and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two flexible opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity within the cell extract. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cell-extract-based high-resolution structural virology. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pe4.cif.gz | 254 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pe4.ent.gz | 206.5 KB | Display | PDB format |
PDBx/mmJSON format | 8pe4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pe4_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8pe4_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8pe4_validation.xml.gz | 65.5 KB | Display | |
Data in CIF | 8pe4_validation.cif.gz | 95.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/8pe4 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/8pe4 | HTTPS FTP |
-Related structure data
Related structure data | 17628MC 8a5tC C: citing same article (ref.) M: map data used to model this data |
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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: 76070.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae virus L-A / References: UniProt: P32503 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Saccharomyces cerevisiae virus L-A / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae virus L-A |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Saccharomyces cerevisiae |
Virus shell | Name: Major gag protein / Diameter: 420 nm |
Buffer solution | pH: 7.4 Details: pH of the buffer was adjusted with NaOH buffer was filtered and sonicated |
Buffer component | Conc.: 200 mM / Name: Ammoniumacetate / Formula: CH3COONH4 |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: heterogenous cell extract |
Specimen support | Details: Plasma Treated, 25 s Sample Negative, 0.4 mbar pressure, 15 mA current Grid material: COPPER / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K / Details: blot force 2 and blot time 6 s before plunging |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 92000 X / Calibrated magnification: 89297 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 118 K / Temperature (min): 77 K |
Image recording | Average exposure time: 3.17 sec. / Electron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 51512 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 7840838 Details: Particles were selected using cryoSPARC blob picker with 500 A diameter and 0.5x diameter inter-particle distance. | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12974 / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: The initial model was rigid-fitted by ChimeraX and refined by iterative cycles of Coot and PHENIX. | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1M1C Accession code: 1M1C / Source name: PDB / Type: experimental model |