National Natural Science Foundation of China (NSFC)
31570736
China
Citation
Journal: PLoS Pathog / Year: 2021 Title: Cryo-EM reveals a previously unrecognized structural protein of a dsRNA virus implicated in its extracellular transmission. Authors: Qianqian Shao / Xudong Jia / Yuanzhu Gao / Zhe Liu / Huan Zhang / Qiqi Tan / Xin Zhang / Huiqiong Zhou / Yinyin Li / De Wu / Qinfen Zhang / Abstract: Mosquito viruses cause unpredictable outbreaks of disease. Recently, several unassigned viruses isolated from mosquitoes, including the Omono River virus (OmRV), were identified as totivirus-like ...Mosquito viruses cause unpredictable outbreaks of disease. Recently, several unassigned viruses isolated from mosquitoes, including the Omono River virus (OmRV), were identified as totivirus-like viruses, with features similar to those of the Totiviridae family. Most reported members of this family infect fungi or protozoans and lack an extracellular life cycle stage. Here, we identified a new strain of OmRV and determined high-resolution structures for this virus using single-particle cryo-electron microscopy. The structures feature an unexpected protrusion at the five-fold vertex of the capsid. Disassociation of the protrusion could result in several conformational changes in the major capsid. All these structures, together with some biological results, suggest the protrusions' associations with the extracellular transmission of OmRV.
Idetical with deposited unit in distinct coordinate
point asymmetric unit, std point frame
Type
Name
Symmetry operation
Number
transform to point frame
1
Symmetry
Point symmetry: (Schoenflies symbol: C5 (5 fold cyclic))
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Components
#1: Protein
Capsidprotein
Mass: 12917.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Omono River virus / Cell line: C6/36 / Strain: LZ / References: UniProt: A0A7M3VBX7*PLUS
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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
-
Sample preparation
Component
Name: Omono River virus / Type: VIRUS Details: Protrusion structure located upon the five-fold vertex of the major capsid. Entity ID: all / Source: NATURAL
Molecular weight
Experimental value: NO
Source (natural)
Organism: Omono River virus / Strain: LZ
Details of virus
Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural host
Organism: Culex quinquefasciatus
Virus shell
Name: Major capsid / Diameter: 450 nm / Triangulation number (T number): 1
Buffer solution
pH: 7.4
Buffer component
ID
Conc.
Name
Formula
Buffer-ID
1
136.89mM
sodiumchoride
NaCl
1
2
2.67mM
potassiumchloride
KCl
1
3
8.1mM
disodiumhydrogenphosphate
Na2HPO4
1
4
1.76mM
potassiumdihydrogenphosphate
KH2PO4
1
Specimen
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Electron dose: 39 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)
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Processing
EM software
ID
Name
Version
Category
2
ETHAN
particleselection
3
EPU
imageacquisition
5
Gctf
CTFcorrection
10
PHENIX
1.17
modelrefinement
11
RELION
initialEulerassignment
12
jspr
finalEulerassignment
13
RELION
3.1
classification
14
RELION
3.1
3Dreconstruction
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
Num. of particles selected: 1160016 Details: Subtracted from every five-fold vertexes from 96668 virus particles. Each virus contains 12 five-fold vertexes. 96668x12=1160016.
Symmetry
Point symmetry: C5 (5 fold cyclic)
3D reconstruction
Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38935 / Symmetry type: POINT
Atomic model building
Protocol: AB INITIO MODEL / Space: REAL
+
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