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- PDB-7qwz: Full capsid of Saccharomyces cerevisiae virus L-BCLa -

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Basic information

Entry
Database: PDB / ID: 7qwz
TitleFull capsid of Saccharomyces cerevisiae virus L-BCLa
ComponentsMajor capsid protein
KeywordsVIRUS / capsid protein dimer / icosahedral asymmetric unit / totivirus capsid
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 virus L-BC
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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 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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Major capsid protein
A: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)156,7882
Polymers156,7882
Non-polymers00
Water00
1
B: Major capsid protein
A: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)9,407,257120
Polymers9,407,257120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

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


Mass: 78393.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae virus L-BC (La) / 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: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
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 FIELD / 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

EM software
IDNameVersionCategoryDetails
1crYOLO1.7.5particle selectioncustom-trained model, detection threshold of 0.5
2SerialEM3.7.14image acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.15model fitting
9PHENIX1.19model refinement
10RELION3.1initial Euler assignmentautorefine
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
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1748 / 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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