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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30539 | |||||||||
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Title | Cryo-EM map of Omono River virus (strain: LZ) empty capsid. | |||||||||
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![]() | Capsid protein != Omono River virus Capsid protein
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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 | single particle reconstruction / cryo EM / Resolution: 3.4 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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 226 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10 KB 10 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 235.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
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Full document | ![]() | 447.6 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Capsid protein
Entire | Name: Capsid protein |
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Components |
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-Supramolecule #1: Omono River virus
Supramolecule | Name: Omono River virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 753758 / Sci species name: Omono River virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: PISADFSEVE NAPSFLSLAE NTDEVLKPYT GLEIQTIITN IVGDANPNQS RIFDQDRLRG NQYSAGGLVT QNAVSAIPFT NLIPRTIRV GNILVNSANR LQITETNVSE YYSNPIIATK LSEMISDQVK NNQFSTWRRD NTSLQGFNAF DIATINTAIL P NGLSLESM ...String: PISADFSEVE NAPSFLSLAE NTDEVLKPYT GLEIQTIITN IVGDANPNQS RIFDQDRLRG NQYSAGGLVT QNAVSAIPFT NLIPRTIRV GNILVNSANR LQITETNVSE YYSNPIIATK LSEMISDQVK NNQFSTWRRD NTSLQGFNAF DIATINTAIL P NGLSLESM LLKLSLLHSI KAMNVDAASI NRSQYQVIDH NTVPTIGAPA VVGVNNSPVF GEDCGGNNPV YPFGGGTGAI AF HVTLQTV PDERKSYAIF VPPAILQATS DANEALALFA LSMSEWPHAL YTVTKQTTDL AGANAGQQVF IPTQSTIHIG GRR VLDLII PRREIAPNPT TLVAANAMCM VRPQAGPDAT AGAIPLAAGQ LFNMNFIGAP AFEEWPMTSY LYSWAGRFDI TTIR QYMGR LATMVGVKDA YWAAHELNVA LSQVAPKMTT AAGGWAAQAA NSAQQSDVCY SSLLTVTRSA ANFPLANQPA ADMRV YDTD PATWNKVALG LATAANLVPE QSMDVPFVVG DARASFWERL QAIPMCIAWT MYYHSRGITT LAWDNAYTDN TNKWLQ KMV RNTFSTTQSV GTIIPARYGK IVCNLYKNMF HRAPAYVATS VGGKELHITH FERWLPGGTY ANVYSGAGAV VNCFSPV LI PDIWCQYFTA KLPLFAGAFP PAQGQNSTKG FNSKQGLMIH RNQNNNLVAP YLEKFADNSS YFPVGQGPEI NDMATWNG R LWMTTGNVQY LDYSGAAIVE AVPPAGELPV GKQIPLLAGE NAPIELTNAA TTCVPRYSND GRRIFTYLTT AQSVIPVQA CNRAANLARS CWLLSNVYAE PALQALGDEV EDAFDTLTNS SFLDVAKSVA ESAGEVPATK ALTDLQAVDV SSLPSTSDPS NVLSQPAPL MSPPTSSS |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |