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- EMDB-30539: Cryo-EM map of Omono River virus (strain: LZ) empty capsid. -

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Basic information

Entry
Database: EMDB / ID: EMD-30539
TitleCryo-EM map of Omono River virus (strain: LZ) empty capsid.
Map data
SampleCapsid protein != Omono River virus

Capsid protein

  • Virus: Omono River virus
    • Protein or peptide: Capsid protein
Function / homologyDouble-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
Function and homology information
Biological speciesOmono River virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShao Q / Jia X / Gao Y / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570736 China
CitationJournal: 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.
History
DepositionSep 11, 2020-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.9
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30539.png

Downloads & links

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Map

FileDownload / File: emd_30539.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 400 pix.
= 568. Å		1.42 Å/pix.
x 400 pix.
= 568. Å		1.42 Å/pix.
x 400 pix.
= 568. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.9 / Movie #1: 2.9
Minimum - Maximum-8.38717 - 14.926134
Average (Standard dev.)-1.772444e-09 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 568.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z568.000568.000568.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-8.38714.926-0.000

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Supplemental data

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Sample components

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Entire : Capsid protein

EntireName: Capsid protein
Components
  • Virus: Omono River virus
    • Protein or peptide: Capsid protein

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Supramolecule #1: Omono River virus

SupramoleculeName: 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

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 19120
CTF correctionSoftware - Name: Gctf
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 15240
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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