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- PDB-7ns2: Virion of Leishmania RNA virus 1 -

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Basic information

Entry
Database: PDB / ID: 7ns2
TitleVirion of Leishmania RNA virus 1
ComponentsCapsid protein
KeywordsVIRUS / Leishmania guyanensis / native virion structure / mucocutaneous leishmaniasis / Totiviridae
Function / homologyTotivirus coat / Totivirus coat protein / Capsid protein
Function and homology information
Biological speciesLeishmania RNA virus 1 - LgM5313
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsProchazkova, M. / Grybchuk, D. / Fuzik, T.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic20-22689S Czech Republic
Citation
Journal: Virology / Year: 2022
Title: Virion structure of Leishmania RNA virus 1.
Authors: Michaela Procházková / Tibor Füzik / Danyil Grybchuk / Vyacheslav Yurchenko / Pavel Plevka /
Abstract: The presence of Leishmania RNA virus 1 (LRV1) enables Leishmania protozoan parasites to cause more severe disease than the virus-free strains. The structure of LRV1 virus-like particles has been ...The presence of Leishmania RNA virus 1 (LRV1) enables Leishmania protozoan parasites to cause more severe disease than the virus-free strains. The structure of LRV1 virus-like particles has been determined previously, however, the structure of the LRV1 virion has not been characterized. Here we used cryo-electron microscopy and single-particle reconstruction to determine the structures of the LRV1 virion and empty particle isolated from Leishmania guyanensis to resolutions of 4.0 Å and 3.6 Å, respectively. The capsid of LRV1 is built from sixty dimers of capsid proteins organized with icosahedral symmetry. RNA genomes of totiviruses are replicated inside the virions by RNA polymerases expressed as C-terminal extensions of a sub-population of capsid proteins. Most of the virions probably contain one or two copies of the RNA polymerase, however, the location of the polymerase domains in LRV1 capsid could not be identified, indicating that it varies among particles. Importance. Every year over 200 000 people contract leishmaniasis and more than five hundred people die of the disease. The mucocutaneous form of leishmaniasis produces lesions that can destroy the mucous membranes of the nose, mouth, and throat. Leishmania parasites carrying Leishmania RNA virus 1 (LRV1) are predisposed to cause aggravated symptoms in the mucocutaneous form of leishmaniasis. Here, we present the structure of the LRV1 virion determined using cryo-electron microscopy.
History
DepositionMar 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.citation_id / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / refine
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _refine.ls_d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)172,8632
Polymers172,8632
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,371,809120
Polymers10,371,809120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein


Mass: 86431.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania RNA virus 1 - LgM5313 / References: UniProt: L7XUU7
Has protein modificationY

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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: Leishmania RNA virus 1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 9.1 MDa / Experimental value: NO
Source (natural)Organism: Leishmania RNA virus 1 / Strain: 1-4
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Leishmania guyanensis / Strain: MHOM/BR/75/M4147
Virus shellName: capsid / Diameter: 421 nm / Triangulation number (T number): 2
Buffer solutionpH: 7.4 / Details: pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESHEPES1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Buffer: 50 mM HEPES pH 7.4, 150 mM NaCl
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE-PROPANE / Humidity: 70 % / Chamber temperature: 295 K

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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: 105000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 3500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3981
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot0.8.9.2model fitting
9PHENIX1.15.2model refinement
12RELIONclassification
13RELION3.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7912
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3768 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 72.61 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: correlation coefficient
Atomic model buildingPDB-ID: 6Y83

6y83


Pdb chain-ID: A / Accession code: 6Y83 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.63 Å

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