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- EMDB-61528: Local refinement of RHDV GI.2 T=1 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-61528
TitleLocal refinement of RHDV GI.2 T=1 VLP
Map data
Sample
  • Virus: Rabbit hemorrhagic disease virus 2
    • Protein or peptide: Capsid protein
KeywordsCalicivirus / viral assembly / rabbit hemorrhagic disease virus (RHDV) / major capsid protein / virus-like particle / VIRAL 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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsRuan Z / Shao Q / Song Y / Hu B / Fan Z / Wei H / Liu Y / Wang F / Fang Q
Funding support China, 4 items
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 Technology FoundationCX(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, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61528.png

Downloads & links

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Map

FileDownload / File: emd_61528.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 120 pix.
= 164.64 Å		1.37 Å/pix.
x 120 pix.
= 164.64 Å		1.37 Å/pix.
x 120 pix.
= 164.64 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.372 Å
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Contour LevelBy AUTHOR: 0.344
Minimum - Maximum-0.023125784 - 2.0799794
Average (Standard dev.)0.013170843 (±0.081020206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 164.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61528_msk_1.map
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Half map: #2

Fileemd_61528_half_map_1.map
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Half map: #1

Fileemd_61528_half_map_2.map
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Sample components

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Entire : Rabbit hemorrhagic disease virus 2

EntireName: Rabbit hemorrhagic disease virus 2
Components
  • Virus: Rabbit hemorrhagic disease virus 2
    • Protein or peptide: Capsid protein

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Supramolecule #1: Rabbit hemorrhagic disease virus 2

SupramoleculeName: Rabbit hemorrhagic disease virus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1930083 / Sci species name: Rabbit hemorrhagic disease virus 2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rabbit hemorrhagic disease virus 2 / Strain: GI.2
Molecular weightTheoretical: 56.900066 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TSVVTTENAS TSIATAGIGG PPQQMDQQET WRTNFYYNDV FTWSVADAPG NILYTVQHSP QNNPFTAVLS QMYAGWAGGM QFRFIVAGS GVFGGRLVAA VIPPGIEIGP GLEVRQFPHV VIDARSLEPV TITMPDLRPN MYHPTGNPGL VPTLVLSVYN N LINPFGGS ...String:
TSVVTTENAS TSIATAGIGG PPQQMDQQET WRTNFYYNDV FTWSVADAPG NILYTVQHSP QNNPFTAVLS QMYAGWAGGM QFRFIVAGS GVFGGRLVAA VIPPGIEIGP GLEVRQFPHV VIDARSLEPV TITMPDLRPN MYHPTGNPGL VPTLVLSVYN N LINPFGGS TSAIQVTVET RPSEDFEFVM IRAPSSKTVD SISPADLLTT PVLTGVGTDN RWNGEIVGLQ PVPGGFSTCN RH WNLNGST YGWSSPRFAA IDHDRGNASF PGSSSSNVLE LWYASAGSAA DNPISQIAPD GFPDMSFVPF SGITIPTAGW VGF GGIWNS SNGAPYVTTM QAYELGFATG VPSNPQPTTT TSGAQIVAKS IYGVANGINQ TTAGLFVMAS GVISTPNSSA TTYT PQPNR IVNAPGTPAA APIGKNTPIM FASVVRRTGD INAEAGSTNG TQYGAGSQPL PVTIGLSLNN YSSALMPGQF FVWQL NFAS GFMELGLSVD GYFYAGTGAS ATLIDLSDLV DIRPVGPRPS TSTLVYNLGG TTNGFSYV

UniProtKB: Capsid protein

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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: 7.2
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 112 / Average exposure time: 5.09 sec. / Average electron dose: 26.09 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 70159
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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