+Open data
-Basic information
Entry | Database: PDB / ID: 6y83 | ||||||
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Title | Capsid structure of Leishmania RNA virus 1 | ||||||
Components | Capsid protein | ||||||
Keywords | VIRUS LIKE PARTICLE / virus-like particle / capsid structure | ||||||
Function / homology | Totivirus coat / Totivirus coat protein / Capsid protein Function and homology information | ||||||
Biological species | Leishmania RNA virus 1 - 4 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å | ||||||
Model details | Virus-like particle assembled from LRV1-4 capsid protein | ||||||
Authors | Prochazkova, M. / Fuzik, T. / Grybtchuk, D. / Falginella, F. / Podesvova, L. / Yurchenko, V. / Vacha, R. / Plevka, P. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6y83.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y83.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 6y83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y83_validation.pdf.gz | 1008 KB | Display | wwPDB validaton report |
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Full document | 6y83_full_validation.pdf.gz | 1021.2 KB | Display | |
Data in XML | 6y83_validation.xml.gz | 46.8 KB | Display | |
Data in CIF | 6y83_validation.cif.gz | 71.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/6y83 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/6y83 | HTTPS FTP |
-Related structure data
Related structure data | 10722MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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 Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Leishmania RNA virus 1 - 4 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Leishmania RNA virus 1 - LgM5313 | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE | |||||||||||||||||||||||||
Natural host | Organism: Leishmania guyanensis / Strain: MHOM/BR/75/M4147 | |||||||||||||||||||||||||
Virus shell | Name: capsid / Diameter: 422 nm / Triangulation number (T number): 2 | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 295 K / Details: blot force 3 blot time 5 wait time 10 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 28000 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16901 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 174 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: R-factor | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1M1C Pdb chain-ID: A / Accession code: 1M1C / Source name: PDB / Type: experimental model |