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- EMDB-39212: Cryo-EM structure of Dragon Grouper nervous necrosis virus-like p... -

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Basic information

Entry
Database: EMDB / ID: EMD-39212
TitleCryo-EM structure of Dragon Grouper nervous necrosis virus-like particle at pH8.0 (3.23A)
Map data
Sample
  • Complex: Dragon Grouper nervous necrosis virus-like particle at pH8.0 (180 subunits)
    • Protein or peptide: Capsid protein alpha
  • Ligand: CALCIUM ION
Keywordsnervous necrosis virus / Dragon Grouper / Cryo-EM structure / VIRUS
Function / homologyNodavirus capsid / nodavirus capsid protein / Viral coat protein subunit / viral capsid / Capsid protein alpha
Function and homology information
Biological speciesDragon grouper nervous necrosis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsWang CH / Chang WH
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: ACS Infect Dis / Year: 2024
Title: Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies a Novel Antiviral Strategy.
Authors: Petra Štěrbová / Chun-Hsiung Wang / Kathleen J D Carillo / Yuan-Chao Lou / Takayuki Kato / Keiichi Namba / Der-Lii M Tzou / Wei-Hau Chang /
Abstract: Many viruses contain surface spikes or protrusions that are essential for virus entry. These surface structures can thereby be targeted by antiviral drugs to treat viral infections. Nervous necrosis ...Many viruses contain surface spikes or protrusions that are essential for virus entry. These surface structures can thereby be targeted by antiviral drugs to treat viral infections. Nervous necrosis virus (NNV), a simple nonenveloped virus in the genus of betanodavirus, infects fish and damages aquaculture worldwide. NNV has 60 conspicuous surface protrusions, each comprising three protrusion domains (P-domain) of its capsid protein. NNV uses protrusions to bind to common receptors of sialic acids on the host cell surface to initiate its entry via the endocytic pathway. However, structural alterations of NNV in response to acidic conditions encountered during this pathway remain unknown, while detailed interactions of protrusions with receptors are unclear. Here, we used cryo-EM to discover that Grouper NNV protrusions undergo low-pH-induced compaction and resting. NMR and molecular dynamics (MD) simulations were employed to probe the atomic details. A solution structure of the P-domain at pH 7.0 revealed a long flexible loop (amino acids 311-330) and a pocket outlined by this loop. Molecular docking analysis showed that the N-terminal moiety of sialic acid inserted into this pocket to interact with conserved residues inside. MD simulations demonstrated that part of this loop converted to a β-strand under acidic conditions, allowing for P-domain trimerization and compaction. Additionally, a low-pH-favored conformation is attained for the linker connecting the P-domain to the NNV shell, conferring resting protrusions. Our findings uncover novel pH-dependent conformational switching mechanisms underlying NNV protrusion dynamics potentially utilized for facilitating NNV entry, providing new structural insights into complex NNV-host interactions with the identification of putative druggable hotspots on the protrusion.
History
DepositionFeb 24, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39212.png

Downloads & links

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Map

FileDownload / File: emd_39212.map.gz / Format: CCP4 / Size: 371.3 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.)
1.16 Å/pix.
x 460 pix.
= 533.6 Å		1.16 Å/pix.
x 460 pix.
= 533.6 Å		1.16 Å/pix.
x 460 pix.
= 533.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.417
Minimum - Maximum-1.3079394 - 3.1913254
Average (Standard dev.)0.032768946 (±0.19220875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-230-230-230
Dimensions460460460
Spacing460460460
CellA=B=C: 533.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39212_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39212_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 : Dragon Grouper nervous necrosis virus-like particle at pH8.0 (180...

EntireName: Dragon Grouper nervous necrosis virus-like particle at pH8.0 (180 subunits)
Components
  • Complex: Dragon Grouper nervous necrosis virus-like particle at pH8.0 (180 subunits)
    • Protein or peptide: Capsid protein alpha
  • Ligand: CALCIUM ION

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Supramolecule #1: Dragon Grouper nervous necrosis virus-like particle at pH8.0 (180...

SupramoleculeName: Dragon Grouper nervous necrosis virus-like particle at pH8.0 (180 subunits)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Dragon grouper nervous necrosis virus

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Macromolecule #1: Capsid protein alpha

MacromoleculeName: Capsid protein alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Dragon grouper nervous necrosis virus
Molecular weightTheoretical: 37.128754 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVRKGEKKLA KPPTTKAANP QPRRRANNRR RSNRTDAPVS KASTVTGFGR GTNDVHLSGM SRISQAVLPA GTGTDGYVVV DATIVPDLL PRLGHAARIF QRYAVETLEF EIQPMCPANT GGGYVAGFLP DPTDNDHTFD ALQATRGAVV AKWWESRTVR P QYTRTLLW ...String:
MVRKGEKKLA KPPTTKAANP QPRRRANNRR RSNRTDAPVS KASTVTGFGR GTNDVHLSGM SRISQAVLPA GTGTDGYVVV DATIVPDLL PRLGHAARIF QRYAVETLEF EIQPMCPANT GGGYVAGFLP DPTDNDHTFD ALQATRGAVV AKWWESRTVR P QYTRTLLW TSSGKEQRLT SPGRLILLCV GNNTDVVNVS VLCRWSVRLS VPSLETPEET TAPIMTQGSL YNDSLSTNDF KS ILLGSTP LDIAPDGAVF QLDRPLSIDY SLGTGDVDRA VYWHLKKFAG NAGTPAGWFR WGIWDNFNKT FTDGVAYYSD EQP RQILLP VGTVCTRVDS EN

UniProtKB: Capsid protein alpha

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 2100F
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7600000000000002 µm / Nominal defocus min: 0.5700000000000001 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40334
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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