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- PDB-6y83: Capsid structure of Leishmania RNA virus 1 -

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Basic information

Entry
Database: PDB / ID: 6y83
TitleCapsid structure of Leishmania RNA virus 1
ComponentsCapsid proteinCapsid
KeywordsVIRUS LIKE PARTICLE / virus-like particle / capsid structure
Function / homologyTotivirus coat / Totivirus coat protein / Capsid protein
Function and homology information
Biological speciesLeishmania RNA virus 1 - 4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å
Model detailsVirus-like particle assembled from LRV1-4 capsid protein
AuthorsProchazkova, M. / Fuzik, T. / Grybtchuk, D. / Falginella, F. / Podesvova, L. / Yurchenko, V. / Vacha, R. / Plevka, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European Research Council (ERC) Czech Republic
CitationJournal: J Virol / Year: 2021
Title: Capsid Structure of RNA Virus 1.
Authors: Michaela Procházková / Tibor Füzik / Danyil Grybchuk / Francesco Luca Falginella / Lucie Podešvová / Vyacheslav Yurchenko / Robert Vácha / Pavel Plevka /
Abstract: parasites cause a variety of symptoms, including mucocutaneous leishmaniasis, which results in the destruction of the mucous membranes of the nose, mouth, and throat. The species of carrying RNA ... parasites cause a variety of symptoms, including mucocutaneous leishmaniasis, which results in the destruction of the mucous membranes of the nose, mouth, and throat. The species of carrying RNA virus 1 (LRV1), from the family , are more likely to cause severe disease and are less sensitive to treatment than those that do not contain the virus. Although the importance of LRV1 for the severity of leishmaniasis was discovered a long time ago, the structure of the virus remained unknown. Here, we present a cryo-electron microscopy reconstruction of the virus-like particle of LRV1 determined to a resolution of 3.65 Å. The capsid has icosahedral symmetry and is formed by 120 copies of a capsid protein assembled in asymmetric dimers. RNA genomes of viruses from the family are synthetized, but not capped at the 5' end, by virus RNA polymerases. To protect viral RNAs from degradation, capsid proteins of the L-A totivirus cleave the 5' caps of host mRNAs, creating decoys to overload the cellular RNA quality control system. Capsid proteins of LRV1 form positively charged clefts, which may be the cleavage sites for the 5' cap of mRNAs. The putative RNA binding site of LRV1 is distinct from that of the related L-A virus. The structure of the LRV1 capsid enables the rational design of compounds targeting the putative decapping site. Such inhibitors may be developed into a treatment for mucocutaneous leishmaniasis caused by LRV1-positive species of Twelve million people worldwide suffer from leishmaniasis, resulting in more than 30 thousand deaths annually. The disease has several variants that differ in their symptoms. The mucocutaneous form, which leads to disintegration of the nasal septum, lips, and palate, is caused predominantly by parasites carrying RNA virus 1 (LRV1). Here, we present the structure of the LRV1 capsid determined using cryo-electron microscopy. Capsid proteins of a related totivirus, L-A virus, protect viral RNAs from degradation by cleaving the 5' caps of host mRNAs. Capsid proteins of LRV1 may have the same function. We show that the LRV1 capsid contains positively charged clefts that may be sites for the cleavage of mRNAs of cells. The structure of the LRV1 capsid enables the rational design of compounds targeting the putative mRNA cleavage site. Such inhibitors may be used as treatments for mucocutaneous leishmaniasis.
History
DepositionMar 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 30, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_src_gen / pdbx_struct_oper_list / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)175,0742
Polymers175,0742
Non-polymers00
Water0
1
A: Capsid protein
B: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,504,432120
Polymers10,504,432120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein / Capsid


Mass: 87536.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Subunit A model for residues 15-204, 210-520, 541-635. Subunit B model for residues 19-290, 300-517, 541-576, 583-642.,Subunit A model for residues 15-204, 210-520, 541-635. Subunit B model ...Details: Subunit A model for residues 15-204, 210-520, 541-635. Subunit B model for residues 19-290, 300-517, 541-576, 583-642.,Subunit A model for residues 15-204, 210-520, 541-635. Subunit B model for residues 19-290, 300-517, 541-576, 583-642.
Source: (gene. exp.) Leishmania RNA virus 1 - 4 / Plasmid: pET42b / Details (production host): C-terminal 8xHis tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7XUU7

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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 - 4 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Leishmania RNA virus 1 - LgM5313
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Leishmania guyanensis / Strain: MHOM/BR/75/M4147
Virus shellName: capsid / Diameter: 422 nm / Triangulation number (T number): 2
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMsodium chlorideNaClSodium chloride1
250 mMTris1
31 mMEDTAEthylenediaminetetraacetic acid1
45 mMbetamercaptoethanolB-me1
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 295 K / Details: blot force 3 blot time 5 wait time 10

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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: 75000 X / Nominal defocus max: 0.5 nm / Nominal defocus min: -0.5 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.5 sec. / Electron dose: 21 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12000

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7PHENIXmodel fitting
9RELION2.1initial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 28000
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16901 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 174 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: R-factor
Atomic model buildingPDB-ID: 1M1C
Pdb chain-ID: A

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