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- EMDB-15823: Chaetoceros socialis forma radians RNA virus 1 full capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-15823
TitleChaetoceros socialis forma radians RNA virus 1 full capsid
Map data
Sample
  • Virus: Chaetoceros socialis forma radians RNA virus 1
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
Keywordspseudo-T=3 / icosahedral / VIRUS
Function / homologyCapsid protein VP4, dicistrovirus / Cricket paralysis virus, VP4 / Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Structural polyprotein
Function and homology information
Biological speciesChaetoceros socialis forma radians RNA virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWang H / Okamoto K / Munke A
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Viruses / Year: 2022
Title: Structural Insights into Common and Host-Specific Receptor-Binding Mechanisms in Algal Picorna-like Viruses.
Authors: Han Wang / Anna Munke / Siqi Li / Yuji Tomaru / Kenta Okamoto /
Abstract: viruses are abundant algal viruses that regulate the dynamics of algal blooms in aquatic environments. They employ a narrow host range because they merely lyse their algal host species. This host- ... viruses are abundant algal viruses that regulate the dynamics of algal blooms in aquatic environments. They employ a narrow host range because they merely lyse their algal host species. This host-specific lysis is thought to correspond to the unique receptor-binding mechanism of the viruses. Here, we present the atomic structures of the full and empty capsids of Chaetoceros socialis forma radians RNA virus 1 built-in 3.0 Å and 3.1 Å cryo-electron microscopy maps. The empty capsid structure and the structural variability provide insights into its assembly and uncoating intermediates. In conjunction with the previously reported atomic model of the Chaetoceros tenuissimus RNA virus type II capsid, we have identified the common and diverse structural features of the VP1 surface between the viruses. We have also tested the potential usage of AlphaFold2 for structural prediction of the VP1s and a subsequent structural phylogeny for classifying viruses by their hosts. These findings will be crucial for inferring the host-specific receptor-binding mechanism in viruses.
History
DepositionSep 16, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15823.png

Downloads & links

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Map

FileDownload / File: emd_15823.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 350 pix.
= 385. Å		1.1 Å/pix.
x 350 pix.
= 385. Å		1.1 Å/pix.
x 350 pix.
= 385. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-1.1823542 - 2.0246959
Average (Standard dev.)0.040316634 (±0.17266792)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 385.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15823_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15823_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Chaetoceros socialis forma radians RNA virus 1

EntireName: Chaetoceros socialis forma radians RNA virus 1
Components
  • Virus: Chaetoceros socialis forma radians RNA virus 1
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein

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Supramolecule #1: Chaetoceros socialis forma radians RNA virus 1

SupramoleculeName: Chaetoceros socialis forma radians RNA virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2169725
Sci species name: Chaetoceros socialis forma radians RNA virus 1
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros socialis forma radians RNA virus 1
Molecular weightTheoretical: 29.930619 KDa
SequenceString: SPLAIAGNRA GGSGAITLEP FGSDNTSPEL SKLHFGETYD HMRVLVKGYN FYKAVLDNTT ITDPDNPSGT VVIRSTVPDF PAPRGHIPN GPDKPFLPHP ENAALCTHLT WFSPCYVARR GGIRWKYLHF GARFGATDAP KGLGFVNRVP QVPYGRRPLG N ERLPLTDV ...String:
SPLAIAGNRA GGSGAITLEP FGSDNTSPEL SKLHFGETYD HMRVLVKGYN FYKAVLDNTT ITDPDNPSGT VVIRSTVPDF PAPRGHIPN GPDKPFLPHP ENAALCTHLT WFSPCYVARR GGIRWKYLHF GARFGATDAP KGLGFVNRVP QVPYGRRPLG N ERLPLTDV NGFNPTELSQ AFSNENGGVY ATDLDVQPAI EVELPFYSSL RFVNPRWDDY EKIGIHRHSI DLLSYRTNGA KC EDAWMAY VAAGDDFNLS WMLSCPPFRL VNL

UniProtKB: Structural polyprotein

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Macromolecule #2: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros socialis forma radians RNA virus 1
Molecular weightTheoretical: 26.871293 KDa
SequenceString: AVKDTIEGNS ETLSGTHQNE TLALYSNVDQ TAVKIMSSID PTRADCVSND HELGNFLSRP VRIMRESISL DERTSTTIAP WDVYLRHPM INKKIANYEY LRANLVLEVV VNGGPFFYGK MLLGYTPFGY EDSLKNFNRI PIGHQNTMLS QQPHVKIDFC E STGGVLHL ...String:
AVKDTIEGNS ETLSGTHQNE TLALYSNVDQ TAVKIMSSID PTRADCVSND HELGNFLSRP VRIMRESISL DERTSTTIAP WDVYLRHPM INKKIANYEY LRANLVLEVV VNGGPFFYGK MLLGYTPFGY EDSLKNFNRI PIGHQNTMLS QQPHVKIDFC E STGGVLHL PFVYNRNYMR ISEGSGEPAS MGELRLNTLN ALKNISFTGP ASSVATITVF AYLDNVELVA PSANDPITAQ QP EL

UniProtKB: Structural polyprotein

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Macromolecule #3: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros socialis forma radians RNA virus 1
Molecular weightTheoretical: 31.098668 KDa
SequenceString: CRPVVIDPPH KYRPTYVGNM ANADIAEAVD KLSLTSKQEL TINHDVIGKK SDGDDMHLST FFGREAYMDR FEWKTTDSYD TLLFYTHVH PILFKRFEAT SGDYDVGMLL PPVGYATIPF SFWRGGMTFR FSIVASAFHR GRLRIVYQPQ GGLGTVPGFS A AFNRVIDL ...String:
CRPVVIDPPH KYRPTYVGNM ANADIAEAVD KLSLTSKQEL TINHDVIGKK SDGDDMHLST FFGREAYMDR FEWKTTDSYD TLLFYTHVH PILFKRFEAT SGDYDVGMLL PPVGYATIPF SFWRGGMTFR FSIVASAFHR GRLRIVYQPQ GGLGTVPGFS A AFNRVIDL GDARDFEVTV EWNQNIAFRE VHTTGSNVPS AQYTPGLDVG RTSQLPLGDQ TSVSNGVLAV YVVNDLVSPD GG TDESVEV NWFVKGAPSF EVASRDTKFA RWSTHWSQEE F

UniProtKB: Structural polyprotein

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3984
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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