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- PDB-7zts: Saccharomyces cerevisiae L-BC virus, open particle, asymmetric re... -

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Basic information

Entry
Database: PDB / ID: 7zts
TitleSaccharomyces cerevisiae L-BC virus, open particle, asymmetric reconstruction
ComponentsMajor capsid protein
KeywordsVIRUS / open particle / totivirus / asymmetric reconstruction
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 BY4741 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16 Å
AuthorsGrybchuk, D. / Prochazkova, M. / Fuzik, T. / Konovalovas, A. / Serva, S. / Yurchenko, V. / Plevka, P.
Funding support Czech Republic, 1items
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 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Major capsid protein
AB: Major capsid protein
AC: Major capsid protein
AD: Major capsid protein
AE: Major capsid protein
AF: Major capsid protein
AG: Major capsid protein
AH: Major capsid protein
AI: Major capsid protein
AJ: Major capsid protein
AK: Major capsid protein
AL: Major capsid protein
AM: Major capsid protein
AN: Major capsid protein
AO: Major capsid protein
AP: Major capsid protein
AQ: Major capsid protein
AR: Major capsid protein
AS: Major capsid protein
AT: Major capsid protein
AU: Major capsid protein
AV: Major capsid protein
AW: Major capsid protein
AX: Major capsid protein
AY: Major capsid protein
AZ: Major capsid protein
BA: Major capsid protein
BB: Major capsid protein
BC: Major capsid protein
BD: Major capsid protein
BE: Major capsid protein
BF: Major capsid protein
BG: Major capsid protein
BH: Major capsid protein
BI: Major capsid protein
BJ: Major capsid protein
BK: Major capsid protein
BL: Major capsid protein
BM: Major capsid protein
BN: Major capsid protein
BO: Major capsid protein
BP: Major capsid protein
BQ: Major capsid protein
BR: Major capsid protein
BS: Major capsid protein
BT: Major capsid protein
BU: Major capsid protein
BV: Major capsid protein
BW: Major capsid protein
BX: Major capsid protein
BY: Major capsid protein
BZ: Major capsid protein
CA: Major capsid protein
CB: Major capsid protein
CC: Major capsid protein
CD: Major capsid protein
CE: Major capsid protein
CF: Major capsid protein
CG: Major capsid protein
CH: Major capsid protein
CI: Major capsid protein
CJ: Major capsid protein
CK: Major capsid protein
CL: Major capsid protein
CM: Major capsid protein
CN: Major capsid protein
CO: Major capsid protein
CP: Major capsid protein
CQ: Major capsid protein
CR: Major capsid protein
CS: Major capsid protein
CT: Major capsid protein
CU: Major capsid protein
CV: Major capsid protein
CW: Major capsid protein
CX: Major capsid protein
CY: Major capsid protein
CZ: Major capsid protein
DA: Major capsid protein
DB: Major capsid protein
DC: Major capsid protein
DD: Major capsid protein
DE: Major capsid protein
DF: Major capsid protein
DG: Major capsid protein
DH: Major capsid protein
DI: Major capsid protein
DJ: Major capsid protein
DK: Major capsid protein
DL: Major capsid protein
DM: Major capsid protein
DN: Major capsid protein
DO: Major capsid protein
DP: Major capsid protein
DQ: Major capsid protein
DR: Major capsid protein
DS: Major capsid protein
DT: Major capsid protein
DU: Major capsid protein
DV: Major capsid protein
DW: Major capsid protein
DX: Major capsid protein
DY: Major capsid protein
DZ: Major capsid protein
EA: Major capsid protein
EB: Major capsid protein
EC: Major capsid protein
ED: Major capsid protein
EE: Major capsid protein
EF: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)8,623,319110
Polymers8,623,319110
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Open particles emerged in two-dimentional classification
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Major capsid protein / Gag protein / Major coat protein


Mass: 78393.812 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4741 (yeast) / References: UniProt: Q87026

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Saccharomyces cerevisiae virus L-BC (La) / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae virus L-BC (La)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Saccharomyces cerevisiae / Strain: BY4741
Virus shellDiameter: 400 nm / Triangulation number (T number): 2
Buffer solutionpH: 7.5 / Details: 20 mM Tris-HCl pH 7.5, 50 mM KCl, 10 mM MgCl2
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Virus was isolated by shearing with glass beads and overnight precipitation in 5% PEG-4000 and 500 mM NaCl
Specimen supportDetails: Glow discharge current 7 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 0, blot time 3 s, 4 C, 100% humidity

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 70 K
Image recordingAverage exposure time: 6 sec. / Electron dose: 36 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11977
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV
Image scansSampling size: 5 µm / Width: 3600 / Height: 3600 / Movie frames/image: 30 / Used frames/image: 1-30

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Linux / Type: package
EM software
IDNameVersionCategoryDetails
1crYOLO1.7.5particle selectioncustom model, 0.5 cut-off
2SerialEM3.7.14image acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.15model fitting
9PHENIX1.19model refinement
10RELION3.1initial Euler assignment3dautorefine
11RELION3.1final Euler assignment3dautorefine
12RELION3.1classification3dclassify with --skip_align option
13RELION3.13D reconstruction3dautorefine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 72705
3D reconstructionResolution: 16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1120 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Initial model generated by RaptorX server

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