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- EMDB-14975: Saccharomyces cerevisiae L-BC virus, open particle, C5 reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-14975
TitleSaccharomyces cerevisiae L-BC virus, open particle, C5 reconstruction
Map dataMain map processed (masked and low-pass filtered to 15 A)
Sample
  • Virus: Saccharomyces cerevisiae virus L-BC (La)
    • Protein or peptide: Major capsid protein
Keywordsopen particle / totivirus / C5 asymmetric unit / VIRUS
Function / homologyMajor coat protein, L-A virus / L-A virus major coat protein superfamily / L-A virus, major coat protein / viral capsid / viral translational frameshifting / RNA binding / Major capsid protein
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae virus L-BC (La)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsGrybchuk D / Prochazkova M / Fuzik T / Konovalovas A / Serva S / Yurchenko V / Plevka P
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGACR-EXPRO GX19-25982X Czech Republic
CitationJournal: Commun Biol / Year: 2022
Title: Structures of L-BC virus and its open particle provide insight into Totivirus capsid assembly.
Authors: Danyil Grybchuk / Michaela Procházková / Tibor Füzik / Aleksandras Konovalovas / Saulius Serva / Vyacheslav Yurchenko / Pavel Plevka /
Abstract: L-BC virus persists in the budding yeast Saccharomyces cerevisiae, whereas other viruses from the family Totiviridae infect a diverse group of organisms including protists, fungi, arthropods, and ...L-BC virus persists in the budding yeast Saccharomyces cerevisiae, whereas other viruses from the family Totiviridae infect a diverse group of organisms including protists, fungi, arthropods, and vertebrates. The presence of totiviruses alters the fitness of the host organisms, for example, by maintaining the killer system in yeast or increasing the virulence of Leishmania guyanensis. Despite the importance of totiviruses for their host survival, there is limited information about Totivirus structure and assembly. Here we used cryo-electron microscopy to determine the structure of L-BC virus to a resolution of 2.9 Å. The L-BC capsid is organized with icosahedral symmetry, with each asymmetric unit composed of two copies of the capsid protein. Decamers of capsid proteins are stabilized by domain swapping of the C-termini of subunits located around icosahedral fivefold axes. We show that capsids of 9% of particles in a purified L-BC sample were open and lacked one decamer of capsid proteins. The existence of the open particles together with domain swapping within a decamer provides evidence that Totiviridae capsids assemble from the decamers of capsid proteins. Furthermore, the open particles may be assembly intermediates that are prepared for the incorporation of the virus (+) strand RNA.
History
DepositionMay 12, 2022-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14975.png

Downloads & links

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Map

FileDownload / File: emd_14975.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map processed (masked and low-pass filtered to 15 A)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 560 pix.
= 603.971 Å		1.08 Å/pix.
x 560 pix.
= 603.971 Å		1.08 Å/pix.
x 560 pix.
= 603.971 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07852 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-3.7178674 - 8.452120000000001
Average (Standard dev.)-0.2291908 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 603.97125 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14975_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: Half-map2

Fileemd_14975_half_map_1.map
AnnotationHalf-map2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half-map1

Fileemd_14975_half_map_2.map
AnnotationHalf-map1
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Saccharomyces cerevisiae virus L-BC (La)

EntireName: Saccharomyces cerevisiae virus L-BC (La)
Components
  • Virus: Saccharomyces cerevisiae virus L-BC (La)
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Saccharomyces cerevisiae virus L-BC (La)

SupramoleculeName: Saccharomyces cerevisiae virus L-BC (La) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Virus was isolated by shearing with glass beads and overnight precipitation in 5% PEG-4000 and 500 mM NaCl
NCBI-ID: 42478 / Sci species name: Saccharomyces cerevisiae virus L-BC (La) / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741
Virus shellShell ID: 1 / Diameter: 400.0 Å / T number (triangulation number): 2

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 78.393812 KDa
SequenceString: MSSLLNSLLP EYFKPKTNLN INSSRVQYGF NARIDMQYED DSGTRKGSRP NAFMSNTVAF IGNYEGIIVD DIPILDGLRA DIFDTHGDL DMGLVEDALS KSTMIRRNVP TYTAYASELL YKRNLTSLFY NMLRLYYIKK WGSIKYEKDA IFYDNGHACL L NRQLFPKS ...String:
MSSLLNSLLP EYFKPKTNLN INSSRVQYGF NARIDMQYED DSGTRKGSRP NAFMSNTVAF IGNYEGIIVD DIPILDGLRA DIFDTHGDL DMGLVEDALS KSTMIRRNVP TYTAYASELL YKRNLTSLFY NMLRLYYIKK WGSIKYEKDA IFYDNGHACL L NRQLFPKS RDASLESSLS LPEAEIAMLD PGLEFPEEDV PAILWHGRVS SRATCILGQA CSEFAPLAPF SIAHYSPQLT RK LFVNAPA GIEPSSGRYT HEDVKDAITI LVSANQAYTD FEAAYLMLAQ TLVSPVPRTA EASAWFINAG MVNMPTLSCA NGY YPALTN VNPYHRLDTW KDTLNHWVAY PDMLFYHSVA MIESCYVELG NVARVSDSDA INKYTFTELS VQGRPVMNRG IIVD LTLVA MRTGREISLP YPVSCGLTRT DALLQGTEIH VPVVVKDIDM PQYYNAIDKD VIEGQETVIK VKQLPPAMYP IYTYG INTT EFYSDHFEDQ VQVEMAPIDN GKAVFNDARK FSKFMSIMRM MGNDVTATDL VTGRKVSNWA DNSSGRFLYT DVKYEG QTA FLVDMDTVKA RDHCWVSIVD PNGTMNLSYK MTNFRAAMFS RNKPLYMTGG SVRTIATGNY RDAAERLRAM DETLRLK PF KITEKLDFRV AAYAIPSLSG SNMPSLHHQE QLQISEVDAE PINPIGEDEL PPDIE

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

Concentration1.5 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl pH 7.5, 50 mM KCl, 10 mM MgCl2
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.007 kPa / Details: Glow discharge current 7 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 0, blot time 3 s, 4 C, 100% humidity.
DetailsVirus was isolated by shearing with glass beads and overnight precipitation in 5% PEG-4000 and 500 mM NaCl

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 80.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3600 pixel / Digitization - Dimensions - Height: 3600 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 11977 / Average exposure time: 6.0 sec. / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 72705
Startup modelType of model: OTHER / Details: Stochastic gradient descent in Relion 3.1
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Software - details: 3dautorefine / Number images used: 1120
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: 3dautorefine
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: 3dautorefine
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1) / Software - details: 3dclassify with --skip_align option
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsInitial model generated by RaptorX server
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7zuf:
Saccharomyces cerevisiae L-BC virus, open particle, C5 reconstruction

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