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- PDB-9jjg: Cryo-EM structure of RHDV GI.2 virion -

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Basic information

Entry
Database: PDB / ID: 9jjg
TitleCryo-EM structure of RHDV GI.2 virion
ComponentsGenome polyprotein
KeywordsVIRUS / Calicivirus / viral assembly / rabbit hemorrhagic disease virus (RHDV) / major capsid protein
Function / homologyCalicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / Capsid protein
Function and homology information
Biological speciesRabbit hemorrhagic disease virus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsRuan, Z. / Shao, Q. / Song, Y. / Hu, B. / Fan, Z. / Wei, H. / Liu, Y. / Wang, F. / Fang, Q.
Funding support China, 4items
OrganizationGrant numberCountry
100 Talents Plan Foundation of Sun Yat-sen University China
China Agriculture Research SystemCARS-43-C-1 China
Jiangsu Provincial Agricultural Science and TechnologyCX(23)1028 China
Shenzhen Science and Technology ProgramZDSYS20230626091203007 China
CitationJournal: J Virol / Year: 2024
Title: Near-atomic structures of RHDV reveal insights into capsid assembly and different conformations between mature virion and VLP.
Authors: Zhiyang Ruan / Qianqian Shao / Yanhua Song / Bo Hu / Zhiyu Fan / Houjun Wei / Yunshu Liu / Fang Wang / Qianglin Fang /
Abstract: Rabbit hemorrhagic disease virus (RHDV) poses a significant threat to rabbits, causing substantial economic losses in rabbit farming. The virus also endangers wild populations of rabbit species and ...Rabbit hemorrhagic disease virus (RHDV) poses a significant threat to rabbits, causing substantial economic losses in rabbit farming. The virus also endangers wild populations of rabbit species and the predatory animals that rely on rabbits as a food source, thereby disturbing the ecological balance. However, the structural understanding of RHDV has been limited due to the lack of high-resolution structures. Here, we present the first high-resolution cryo-EM structures of the mature virion and virus-like particles (VLPs) derived from both full-length and N-terminal arm (NTA)-truncated VP60. These structures reveal intricate structural details of the icosahedral capsid and crucial NTA-mediated interactions essential for capsid assembly. In addition, dramatic conformational differences are unexpectedly observed between the mature virion and VLP. The protruding spikes of the A-B dimers adopt a "raised" state in the mature virion and a "resting" state in the VLP. These findings enhance our understanding of the structure, assembly, and conformational dynamics of the RHDV capsid, laying the essential groundwork for further virological research and therapeutic advancements.IMPORTANCERHDV is a pathogen with significant economic and ecological impact. By presenting the first high-resolution cryo-EM structures of RHDV, we have uncovered detailed interactions among neighboring VP60 subunits of the icosahedral capsid. The NTA of VP60 is uniquely clustered around the threefold axis of the capsid, probably play a critical role in dragging the six VP60 dimers around the threefold axis during capsid assembly. Additionally, we observed dramatic conformational differences between the mature virion and VLPs. VLPs are commonly used for vaccine development, under the assumption that their structure closely resembles that of the mature virion. Our findings significantly advance the understanding of the RHDV capsid structure, which may be used for developing potential therapeutic strategies against RHDV.
History
DepositionSep 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Dec 4, 2024Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update
Revision 1.3Jan 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)181,2603
Polymers181,2603
Non-polymers00
Water00
1
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Theoretical massNumber of molelcules
Total (without water)10,875,587180
Polymers10,875,587180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Genome polyprotein / p254


Mass: 60419.926 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabbit hemorrhagic disease virus 2 / Strain: GI.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A3S8Q1D6
Has protein modificationN

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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: Rabbit hemorrhagic disease virus 2 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rabbit hemorrhagic disease virus 2
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: sf9
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 410 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.09 sec. / Electron dose: 26.09 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 270

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
10RELION4initial Euler assignment
11RELION4final Euler assignment
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 33634
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21493 / Symmetry type: POINT

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