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- PDB-8yf8: Cryo-EM structure of Dragon Grouper nervous necrosis virus-like p... -

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Entry
Database: PDB / ID: 8yf8
TitleCryo-EM structure of Dragon Grouper nervous necrosis virus-like particle at pH5.0 (3.52A)
ComponentsCapsid protein alpha
KeywordsVIRUS / nervous necrosis virus / Dragon Grouper / Cryo-EM structure
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsWang, C.H. / Chang, W.H.
Funding support Taiwan, 2items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein alpha
B: Capsid protein alpha
C: Capsid protein alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5066
Polymers111,3863
Non-polymers1203
Water00
1
A: Capsid protein alpha
B: Capsid protein alpha
C: Capsid protein alpha
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,690,390360
Polymers6,683,176180
Non-polymers7,214180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein alpha
B: Capsid protein alpha
C: Capsid protein alpha
hetero molecules
x 5


  • icosahedral pentamer
  • 558 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)557,53230
Polymers556,93115
Non-polymers60115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein alpha
B: Capsid protein alpha
C: Capsid protein alpha
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 669 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)669,03936
Polymers668,31818
Non-polymers72118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein alpha


Mass: 37128.754 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dragon grouper nervous necrosis virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9E6H7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dragon Grouper nervous necrosis virus-like particle at pH5.0 (180 subunits)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Dragon grouper nervous necrosis virus
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 2100F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2930 nm / Nominal defocus min: 870 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22364 / Symmetry type: POINT

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