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- EMDB-17628: Capsid structure of the L-A helper virus from native viral communities -

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Basic information

Entry
Database: EMDB / ID: EMD-17628
TitleCapsid structure of the L-A helper virus from native viral communities
Map dataIcosahedrally refined cryo-EM map of the L-A helper virus.
Sample
  • Virus: Saccharomyces cerevisiae virus L-A
    • Protein or peptide: Major capsid protein
KeywordsCapsid structure ScVLA / viral particle / wildtype / endogenous / VIRUS
Function / homologyMajor 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 speciesSaccharomyces cerevisiae virus L-A
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsSchmidt L / Tueting C / Kyrilis F / Hamdi F / Semchonok DA / Kastritis PL
Funding support Germany, European Union, 6 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
European Research Council (ERC)101086665European Union
CitationJournal: 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
DepositionJun 13, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17628.png

Downloads & links

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Map

FileDownload / File: emd_17628.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedrally refined cryo-EM map of the L-A helper virus.
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.13738306 - 0.36944014
Average (Standard dev.)0.00053186563 (±0.025054554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 651.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Icosahedrally refined cryo-EM map of the L-A helper...

Fileemd_17628_additional_1.map
AnnotationIcosahedrally refined cryo-EM map of the L-A helper virus. Sharpened by cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Icosahedrally refined cryo-EM map of the L-A helper...

Fileemd_17628_half_map_1.map
AnnotationIcosahedrally refined cryo-EM map of the L-A helper virus. Half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Icosahedrally refined cryo-EM map of the L-A helper...

Fileemd_17628_half_map_2.map
AnnotationIcosahedrally refined cryo-EM map of the L-A helper virus. Half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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
    • Protein or peptide: Major capsid protein

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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: all / 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)
Virus shellShell ID: 1 / Name: Major gag protein / Diameter: 420.0 Å

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae virus L-A
Molecular weightTheoretical: 76.070031 KDa
SequenceString: MLRFVTKNSQ DKSSDLFSIC SDRGTFVAHN RVRTDFKFDN LVFNRVYGVS QKFTLVGNPT VCFNEGSSYL EGIAKKYLTL DGGLAIDNV LNELRSTCGI PGNAVASHAY NITSWRWYDN HVALLMNMLR AYHLQVLTEQ GQYSAGDIPM YHDGHVKIKL P VTIDDTAG ...String:
MLRFVTKNSQ DKSSDLFSIC SDRGTFVAHN RVRTDFKFDN LVFNRVYGVS QKFTLVGNPT VCFNEGSSYL EGIAKKYLTL DGGLAIDNV LNELRSTCGI PGNAVASHAY NITSWRWYDN HVALLMNMLR AYHLQVLTEQ GQYSAGDIPM YHDGHVKIKL P VTIDDTAG PTQFAWPSDR STDSYPDWAQ FSESFPSIDV PYLDVRPLTV TEVNFVLMMM SKWHRRTNLA IDYEAPQLAD KF AYRHALT VQDADEWIEG DRTDDQFRPP SSKVMLSALR KYVNHNRLYN QFYTAAQLLA QIMMKPVPNC AEGYAWLMHD ALV NIPKFG SIRGRYPFLL SGDAALIQAT ALEDWSAIMA KPELVFTYAM QVSVALNTGL YLRRVKKTGF GTTIDDSYED GAFL QPETF VQAALACCTG QDAPLNGMSD VYVTYPDLLE FDAVTQVPIT VIEPAGYNIV DDHLVVVGVP VACSPYMIFP VAAFD TANP YCGNFVIKAA NKYLRKGAVY DKLEAWKLAW ALRVAGYDTH FKVYGDTHGL TKFYADNGDT WTHIPEFVTD GDVMEV FVT AIERRARHFV ELPRLNSPAF FRSVEVSTTI YDTHVQAGAH AVYHASRINL DYVKPVSTGI QVINAGELKN YWGSVRR TQ QGLGVVGLTM PAVMPTGEPT AGAAHEELIE QADNVLVE

UniProtKB: Major capsid protein

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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: PLASMA CLEANING / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa
Details: Plasma Treated, 25 s Sample Negative, 0.4 mbar pressure, 15 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 2 and blot time 6 s before plunging.
Detailsheterogenous cell extract

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 89297 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.0 K / Max: 118.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 51512 / Average exposure time: 3.17 sec. / Average electron dose: 30.0 e/Å2

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Image processing

Particle selectionNumber selected: 7840838
Details: Particles were selected using cryoSPARC blob picker with 500 A diameter and 0.5x diameter inter-particle distance.
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 2 / Avg.num./class: 10000 / Software - Name: cryoSPARC (ver. v3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3) / Number images used: 12974
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1m1c


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe initial model was rigid-fitted by ChimeraX and refined by iterative cycles of Coot and PHENIX.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8pe4:
Capsid structure of the L-A helper virus from native viral communities

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