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- EMDB-15214: Endogenous yeast L-A helper virus identified from native cell extracts -

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Basic information

Entry
Database: EMDB / ID: EMD-15214
TitleEndogenous yeast L-A helper virus identified from native cell extracts
Map dataIcosahedrally averaged capsid of the L-A helper virus from native Saccharomyces cerevisiae cell extract
Sample
  • Virus: Saccharomyces cerevisiae virus L-A
KeywordsCapsid structure ScVLA / viral particle / wildtype / endogenous / VIRUS
Biological speciesSaccharomyces cerevisiae virus L-A
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsSchmidt L / Kyrilis F / Hamdi F / Semchonok DA / Kastritis PL
Funding support Germany, European Union, 5 items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research03Z22HN23 Germany
German Federal Ministry for Education and Research03Z22HI2 Germany
German Federal Ministry for Education and Research03COV04 Germany
German Research Foundation (DFG)391498659 Germany
European Regional Development FundEFRE: ZS/2016/04/78115European Union
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.
#1: Journal: Biorxiv / Year: 2022
Title: Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts
Authors: Schmidt L / Tuting C / Kyrilis FL / Hamdi F / Semchonok DA / Hause G / Meister A / Ihling C / Shah PNM / Stubbs MT / Sinz A / Stuart DI / Kastritis PL
History
DepositionJun 20, 2022-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15214.png

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Map

FileDownload / File: emd_15214.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedrally averaged capsid of the L-A helper virus from native Saccharomyces cerevisiae cell extract
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
3.18 Å/pix.
x 256 pix.
= 813.312 Å		3.18 Å/pix.
x 256 pix.
= 813.312 Å		3.18 Å/pix.
x 256 pix.
= 813.312 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.177 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.177
Minimum - Maximum-0.048667323 - 0.27428097
Average (Standard dev.)0.0027091103 (±0.019830445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 813.312 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15214_msk_1.map
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Additional map: Asymmetrically reconstructed inner density of the L-A helper...

Fileemd_15214_additional_1.map
AnnotationAsymmetrically reconstructed inner density of the L-A helper virus revealing location of viral RNA
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Half map: Icosahedrally averaged capsid of the L-A helper virus...

Fileemd_15214_half_map_1.map
AnnotationIcosahedrally averaged capsid of the L-A helper virus from native Saccharomyces cerevisiae cell extract - Half Map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Icosahedrally averaged capsid of the L-A helper virus...

Fileemd_15214_half_map_2.map
AnnotationIcosahedrally averaged capsid of the L-A helper virus from native Saccharomyces cerevisiae cell extract - Half Map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Saccharomyces cerevisiae virus L-A

EntireName: Saccharomyces cerevisiae virus L-A
Components
  • Virus: Saccharomyces cerevisiae virus L-A

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Supramolecule #1: Saccharomyces cerevisiae virus L-A

SupramoleculeName: Saccharomyces cerevisiae virus L-A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 11008 / Sci species name: Saccharomyces cerevisiae virus L-A / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4 / Component - Concentration: 200.0 mM / Component - Formula: CH3COONH4 / Component - Name: Ammoniumacetate
Details: pH of the buffer was adjusted with NaOH buffer was filtered and sonicated
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 2 and blot time 6 before plunging.
Detailsheterogenous cell extract

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Electron microscopy

MicroscopeTFS GLACIOS
TemperatureMin: 77.0 K / Max: 118.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 7 / Number real images: 10067 / Average exposure time: 3.61 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 44067 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1020420
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Scipion (ver. v.3.0.10) / Number images used: 17000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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