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- EMDB-10087: Acquired functional capsid structures in metazoan totivirus-like ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10087
TitleAcquired functional capsid structures in metazoan totivirus-like dsRNA virus.
Map dataOmono River virus capsid
Sample
  • Virus: Omono River virus
    • Protein or peptide: Capsid protein
    • Protein or peptide: Capsid protein
KeywordsMosquito / Totivirus / Totiviridae / Totivirus-like virus / dsRNA / capsid / VIRUS
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 / Capsid protein
Function and homology information
Biological speciesOmono River virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsOkamoto K / Larsson SDD
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research Council2018-03387 Sweden
Swedish Research Council2018-00421 Sweden
Swedish Research CouncilJA2014-5721 Sweden
CitationJournal: Structure / Year: 2020
Title: Acquired Functional Capsid Structures in Metazoan Totivirus-like dsRNA Virus.
Authors: Kenta Okamoto / Ricardo J Ferreira / Daniel S D Larsson / Filipe R N C Maia / Haruhiko Isawa / Kyoko Sawabe / Kazuyoshi Murata / Janos Hajdu / Kenji Iwasaki / Peter M Kasson / Naoyuki Miyazaki /
Abstract: Non-enveloped icosahedral double-stranded RNA (dsRNA) viruses possess multifunctional capsids required for their proliferation. Whereas protozoan/fungal dsRNA viruses have a relatively simple capsid ...Non-enveloped icosahedral double-stranded RNA (dsRNA) viruses possess multifunctional capsids required for their proliferation. Whereas protozoan/fungal dsRNA viruses have a relatively simple capsid structure, which suffices for the intracellular phase in their life cycle, metazoan dsRNA viruses have acquired additional structural features as an adaptation for extracellular cell-to-cell transmission in multicellular hosts. Here, we present the first atomic model of a metazoan dsRNA totivirus-like virus and the structure reveals three unique structural traits: a C-terminal interlocking arm, surface projecting loops, and an obstruction at the pore on the 5-fold symmetry axis. These traits are keys to understanding the capsid functions of metazoan dsRNA viruses, such as particle stability and formation, cell entry, and endogenous intraparticle transcription of mRNA. On the basis of molecular dynamics simulations of the obstructed pore, we propose a possible mechanism of intraparticle transcription in totivirus-like viruses, which dynamically switches between open and closed states of the pore(s).
History
DepositionJun 20, 2019-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 150
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 150
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6s2c
  • Surface level: 150
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6s2c
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10087.png

Downloads & links

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Map

FileDownload / File: emd_10087.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOmono River virus capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 500 pix.
= 560. Å		1.12 Å/pix.
x 500 pix.
= 560. Å		1.12 Å/pix.
x 500 pix.
= 560. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 150.0 / Movie #1: 150
Minimum - Maximum-1125.34050000000002 - 1326.149400000000014
Average (Standard dev.)0.45599967 (±75.891840000000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin767676
Dimensions500500500
Spacing500500500
CellA=B=C: 560.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z560.000560.000560.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS767676
NC/NR/NS500500500
D min/max/mean-1125.3401326.1490.456

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Supplemental data

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Sample components

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Entire : Omono River virus

EntireName: Omono River virus
Components
  • Virus: Omono River virus
    • Protein or peptide: Capsid protein
    • 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
Details: Omono River virus particles from C6/36 mosquito cells
NCBI-ID: 753758 / Sci species name: Omono River virus / Sci species strain: AK4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Aedes (mosquito)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 420.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Omono River virus
Molecular weightTheoretical: 91.202719 KDa
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 AFEEWPLTSY LYSWAGRFDI TTIR QYMGR LATMVGVKDA YWAAHELNVA LSQVAPKMTT AAGGWAAQAA NSAQQSDVCY SSLLTVTRSA ANFPLANQPA ADMRV YDTD PATWNKVALG LATAANLVPE QSMDVPFVVG DARTSFWERL 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

UniProtKB: Capsid protein

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Macromolecule #2: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Omono River virus
Molecular weightTheoretical: 91.436969 KDa
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 AFEEWPLTSY LYSWAGRFDI TTIR QYMGR LATMVGVKDA YWAAHELNVA LSQVAPKMTT AAGGWAAQAA NSAQQSDVCY SSLLTVTRSA ANFPLANQPA ADMRV YDTD PATWNKVALG LATAANLVPE QSMDVPFVVG DARTSFWERL 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 SF

UniProtKB: Capsid protein

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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

Concentration1.4 mg/mL
BufferpH: 7.5 / Component - Concentration: 100.0 mM / Component - Formula: C2H7NO2 / Component - Name: ammonium acetate
GridMaterial: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Number real images: 4521 / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.225 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 30986
Startup modelType of model: EMDB MAP
EMDB ID:

3350


Details: Omono River virus
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 2.1), jspr) / Number images used: 30363
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient
Output model

PDB-6s2c:
Acquired functional capsid structures in metazoan totivirus-like dsRNA virus.

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