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.
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
Experiment
Method: ELECTRON MICROSCOPY
EM experiment
Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
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
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Processing
EM software
ID
Name
Version
Category
2
EPU
imageacquisition
4
CTFFIND
4
CTFcorrection
7
PHENIX
modelfitting
9
RELION
2.1
initialEulerassignment
10
RELION
finalEulerassignment
11
RELION
classification
12
RELION
3Dreconstruction
13
PHENIX
modelrefinement
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
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