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- PDB-7d0l: The major capsid of Omono River virus (strain:LZ), protrusion-fre... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d0l | ||||||
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Title | The major capsid of Omono River virus (strain:LZ), protrusion-free status. | ||||||
![]() | Capsid protein | ||||||
![]() | VIRUS / Totiviridae / major capsid / viral protein | ||||||
Function / homology | Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / RNA binding / Main capsid protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å | ||||||
![]() | Shao, Q. / Jia, X. / Gao, Y. / Liu, Z. | ||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 305.6 KB | Display | ![]() |
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PDB format | ![]() | 234.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30538MC ![]() 7cz6C ![]() 7d0kC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
| x 60
2 |
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3 | ![]()
| x 5
4 | ![]()
| x 6
5 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 96860.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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 |
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Sample preparation
Component | Name: Major capsid dimer of OmRV-LZ (protrusion-free status) Type: VIRUS / Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
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 |
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Specimen | 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 R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: NONE |
Specimen holder | Cryogen: NITROGEN |
Image recording | 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 |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 96668 Details: Subtracted from every five-fold vertexes from 96668 virus particles. Each virus contains 12 five-fold vertexes. 96668x12=1160016. | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15240 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |