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- EMDB-14194: Empty capsid of Saccharomyces cerevisiae virus L-BCLa -

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Basic information

Entry
Database: EMDB / ID: EMD-14194
TitleEmpty capsid of Saccharomyces cerevisiae virus L-BCLa
Map data
Sample
  • Virus: Saccharomyces cerevisiae virus L-BC (La)
    • Protein or peptide: Major capsid protein
Function / homologyMajor coat protein, L-A virus / L-A virus major coat protein superfamily / L-A virus, major coat protein / viral capsid / RNA binding / Major capsid protein
Function and homology information
Biological speciesSaccharomyces cerevisiae virus L-BC (La)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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 RepublicGX19-25982X 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
DepositionJan 26, 2022-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateSep 7, 2022-
Current statusSep 7, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14194.png

Downloads & links

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Map

FileDownload / File: emd_14194.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 420 pix.
= 453.18 Å		1.08 Å/pix.
x 420 pix.
= 453.18 Å		1.08 Å/pix.
x 420 pix.
= 453.18 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.079 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.92
Minimum - Maximum-9.07824 - 15.217176
Average (Standard dev.)-6.8108523e-09 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 453.18 Å
α=β=γ: 90.0 °

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Supplemental data

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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 / NCBI-ID: 42478 / Sci species name: Saccharomyces cerevisiae virus L-BC (La) / Virus type: VIRION / Virus isolate: SPECIES / 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae virus L-BC (La)
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

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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 - 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 80.0 K
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 - Sampling interval: 5.0 µm / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 72705
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER / Details: Stochastic gradient descent in Relion 3.1
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: autorefine
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1) / Software - details: 3dclassify with --skip_align option
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: 3dautorefine
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Software - details: 3dautorefine / Number images used: 38763
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-7qwx:
Empty capsid of Saccharomyces cerevisiae virus L-BCLa

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