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- EMDB-39217: Cryo-EM structure of Dragon Grouper nervous necrosis virion at pH... -

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Basic information

Entry
Database: EMDB / ID: EMD-39217
TitleCryo-EM structure of Dragon Grouper nervous necrosis virion at pH5.0 (4.36A)
Map data
Sample
  • Complex: Dragon Grouper nervous necrosis virion at pH5.0 (180 subunits)
    • Protein or peptide: Dragon Grouper nervous necrosis virion at pH5.0
Keywordsnervous necrosis virus / Dragon Grouper / Cryo-EM structure / VIRUS
Biological speciesChanna striata (snakehead murrel)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.36 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_39217.png

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Map

FileDownload / File: emd_39217.map.gz / Format: CCP4 / Size: 216 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.)
1.09 Å/pix.
x 384 pix.
= 418.099 Å		1.09 Å/pix.
x 384 pix.
= 418.099 Å		1.09 Å/pix.
x 384 pix.
= 418.099 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0888 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.27817932 - 1.077031
Average (Standard dev.)0.08629442 (±0.15666011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-191-191-191
Dimensions384384384
Spacing384384384
CellA=B=C: 418.09918 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39217_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dragon Grouper nervous necrosis virion at pH5.0 (180 subunits)

EntireName: Dragon Grouper nervous necrosis virion at pH5.0 (180 subunits)
Components
  • Complex: Dragon Grouper nervous necrosis virion at pH5.0 (180 subunits)
    • Protein or peptide: Dragon Grouper nervous necrosis virion at pH5.0

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Supramolecule #1: Dragon Grouper nervous necrosis virion at pH5.0 (180 subunits)

SupramoleculeName: Dragon Grouper nervous necrosis virion at pH5.0 (180 subunits)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Channa striata (snakehead murrel) / Strain: SSN-1 cell

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Macromolecule #1: Dragon Grouper nervous necrosis virion at pH5.0

MacromoleculeName: Dragon Grouper nervous necrosis virion at pH5.0 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MVRKGEKKLA KPPTTKAANP QPRRRANNRR RSNRTDAPVS KASTVTGFGR GTNDVHLSGM SRISQAVLPA GTGTDGYVVV DATIVPDLLP RLGHAARIFQ RYAVETLEFE IQPMCPANTG GGYVAGFLPD PTDNDHTFDA LQATRGAVVA KWWESRTVRP QYTRTLLWTS ...String:
MVRKGEKKLA KPPTTKAANP QPRRRANNRR RSNRTDAPVS KASTVTGFGR GTNDVHLSGM SRISQAVLPA GTGTDGYVVV DATIVPDLLP RLGHAARIFQ RYAVETLEFE IQPMCPANTG GGYVAGFLPD PTDNDHTFDA LQATRGAVVA KWWESRTVRP QYTRTLLWTS SGKEQRLTSP GRLILLCVGN NTDVVNVSVL CRWSVRLSVP SLETPEETTA PIMTQGSLYN DSLSTNDFKS ILLGSTPLDI APDGAVFQLD RPLSIDYSLG TGDVDRAVYW HLKKFAGNAG TPAGWFRWGI WDNFNKTFTD GVAYYSDEQP RQILLPVGTV CTRVDSEN

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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: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.18 µm / Nominal defocus min: 0.42 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26494
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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