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- EMDB-33810: Structure of the Spring Viraemia of Carp Virus ribonucleoprotein ... -

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Entry
Database: EMDB / ID: EMD-33810
TitleStructure of the Spring Viraemia of Carp Virus ribonucleoprotein Complex
Map data
Sample
  • Complex: ribonucleoprotein complex of the spring viraemia carp virus
    • Complex: nucleoprotein
      • Protein or peptide: Nucleoprotein
    • Complex: RNA
      • RNA: RNA (99-mer)
KeywordsRibonucleoprotein / Complex / VIRUS / VIRUS LIKE PARTICLE-RNA complex
Biological speciesSprivirus cyprinus / Trichoplusia ni (cabbage looper) / Sprivivirus cyprinus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLiu B / Wang ZX / Yang T / Yu DQ / Ouyang Q
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725026 China
National Natural Science Foundation of China (NSFC)82225028 China
National Natural Science Foundation of China (NSFC)82172287 China
CitationJournal: J Virol / Year: 2023
Title: Structure of the Spring Viraemia of Carp Virus Ribonucleoprotein Complex Reveals Its Assembly Mechanism and Application in Antiviral Drug Screening.
Authors: Zhao-Xi Wang / Bing Liu / Tian Yang / Daqi Yu / Chu Zhang / Liming Zheng / Jin Xie / Bin Liu / Mengxi Liu / Hailin Peng / Luhua Lai / Qi Ouyang / Songying Ouyang / Yong-An Zhang /
Abstract: Spring viremia of carp virus (SVCV) is a highly pathogenic infecting the common carp, yet neither a vaccine nor effective therapies are available to treat spring viremia of carp (SVC). Like all ...Spring viremia of carp virus (SVCV) is a highly pathogenic infecting the common carp, yet neither a vaccine nor effective therapies are available to treat spring viremia of carp (SVC). Like all negative-sense viruses, SVCV contains an RNA genome that is encapsidated by the nucleoprotein (N) in the form of a ribonucleoprotein (RNP) complex, which serves as the template for viral replication and transcription. Here, the three-dimensional (3D) structure of SVCV RNP was resolved through cryo-electron microscopy (cryo-EM) at a resolution of 3.7 Å. RNP assembly was stabilized by N and C loops; RNA was wrapped in the groove between the N and C lobes with 9 nt nucleotide per protomer. Combined with mutational analysis, our results elucidated the mechanism of RNP formation. The RNA binding groove of SVCV N was used as a target for drug virtual screening, and it was found suramin had a good antiviral effect. This study provided insights into RNP assembly, and anti-SVCV drug screening was performed on the basis of this structure, providing a theoretical basis and efficient drug screening method for the prevention and treatment of SVC. Aquaculture accounts for about 70% of global aquatic products, and viral diseases severely harm the development of aquaculture industry. Spring viremia of carp virus (SVCV) is the pathogen causing highly contagious spring viremia of carp (SVC) disease in cyprinids, especially common carp (), yet neither a vaccine nor effective therapies are available to treat this disease. In this study, we have elucidated the mechanism of SVCV ribonucleoprotein complex (RNP) formation by resolving the 3D structure of SVCV RNP and screened antiviral drugs based on the structure. It is found that suramin could competitively bind to the RNA binding groove and has good antiviral effects both and . Our study provides a template for rational drug discovery efforts to treat and prevent SVCV infections.
History
DepositionJul 11, 2022-
Header (metadata) releaseMar 15, 2023-
Map releaseMar 15, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33810.png

Downloads & links

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Map

FileDownload / File: emd_33810.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 168 pix.
= 230.16 Å		1.37 Å/pix.
x 168 pix.
= 230.16 Å		1.37 Å/pix.
x 168 pix.
= 230.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0271
Minimum - Maximum-0.17290473 - 0.32962015
Average (Standard dev.)0.0010094885 (±0.012184945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 230.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33810_msk_1.map
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Half map: #2

Fileemd_33810_half_map_1.map
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Half map: #1

Fileemd_33810_half_map_2.map
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Sample components

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Entire : ribonucleoprotein complex of the spring viraemia carp virus

EntireName: ribonucleoprotein complex of the spring viraemia carp virus
Components
  • Complex: ribonucleoprotein complex of the spring viraemia carp virus
    • Complex: nucleoprotein
      • Protein or peptide: Nucleoprotein
    • Complex: RNA
      • RNA: RNA (99-mer)

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Supramolecule #1: ribonucleoprotein complex of the spring viraemia carp virus

SupramoleculeName: ribonucleoprotein complex of the spring viraemia carp virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sprivirus cyprinus

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Supramolecule #2: nucleoprotein

SupramoleculeName: nucleoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Trichoplusia ni (cabbage looper)

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Sprivivirus cyprinus
Molecular weightTheoretical: 46.62116 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: RIKTNAAVAA VLPANEDQAD YPSTFFEGGN EIRLYVNRGE KLDVLRQYVY MGLVEKNCRI QHVNAYLYAV LKGERELLEA DWDSFGHKI GIQGDKIGPF NLVRVEDIPD GLPDGKLNAE VSAEDDAWLP LFLLGLYRVG RASETAYRTL LMESLIKQCK A IKSDWVSP ...String:
RIKTNAAVAA VLPANEDQAD YPSTFFEGGN EIRLYVNRGE KLDVLRQYVY MGLVEKNCRI QHVNAYLYAV LKGERELLEA DWDSFGHKI GIQGDKIGPF NLVRVEDIPD GLPDGKLNAE VSAEDDAWLP LFLLGLYRVG RASETAYRTL LMESLIKQCK A IKSDWVSP VTATHKYFDV WGNDGNYLKI VACVDMFYNH FKKSIKATFR WGTIVSRFKD CAALATLGHV VKITGLTIEE VF TWVLQTE VADELVKMMK PGQEIDKSTS YMPYLIDMGI SAKSPYSTIK NPSFHFWGQL VAALCRSKRA LNARQPDEID SMS ISNASL LMAYALGSSP DIEQQFSTGN TYRKPPKEAS YLVSEEPKNR SVVEWIAWYS DVDNKPTDDM LMMAKRVAGT ISGP RDNSV GKWIKQTYG

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Macromolecule #2: RNA (99-mer)

MacromoleculeName: RNA (99-mer) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 30.26548 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUU UUUUUUUUUU

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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

Concentration0.5 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2gic

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 614458
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7yg7:
Structure of the Spring Viraemia of Carp Virus ribonucleoprotein Complex

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