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- EMDB-61529: Cryo-EM structure of a T=3 VLP of RHDV GI.2 -

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Basic information

Entry
Database: EMDB / ID: EMD-61529
TitleCryo-EM structure of a T=3 VLP of RHDV GI.2
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 / VIRUS LIKE PARTICLE
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: 2.45 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 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, 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_61529.png

Downloads & links

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Map

FileDownload / File: emd_61529.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 576 pix.
= 618.624 Å		1.07 Å/pix.
x 576 pix.
= 618.624 Å		1.07 Å/pix.
x 576 pix.
= 618.624 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
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Contour LevelBy AUTHOR: 0.0117
Minimum - Maximum-0.05151717 - 0.0854436
Average (Standard dev.)-0.000017880733 (±0.004514214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 618.624 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61529_msk_1.map
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Half map: #1

Fileemd_61529_half_map_1.map
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Half map: #2

Fileemd_61529_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
Virus shellShell ID: 1 / Diameter: 410.0 Å / T number (triangulation number): 3

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rabbit hemorrhagic disease virus 2 / Strain: GI.2
Molecular weightTheoretical: 60.419926 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEGKARATPQ GETAGTATTA SVPGTTTDGM DPGVVATTSV VTTENASTSI ATAGIGGPPQ QMDQQETWRT NFYYNDVFTW SVADAPGNI LYTVQHSPQN NPFTAVLSQM YAGWAGGMQF RFIVAGSGVF GGRLVAAVIP PGIEIGPGLE VRQFPHVVID A RSLEPVTI ...String:
MEGKARATPQ GETAGTATTA SVPGTTTDGM DPGVVATTSV VTTENASTSI ATAGIGGPPQ QMDQQETWRT NFYYNDVFTW SVADAPGNI LYTVQHSPQN NPFTAVLSQM YAGWAGGMQF RFIVAGSGVF GGRLVAAVIP PGIEIGPGLE VRQFPHVVID A RSLEPVTI TMPDLRPNMY HPTGNPGLVP TLVLSVYNNL INPFGGSTSA IQVTVETRPS EDFEFVMIRA PSSKTVDSIS PA DLLTTPV LTGVGTDNRW NGEIVGLQPV PGGFSTCNRH WNLNGSTYGW SSPRFAAIDH DRGNASFPGS SSSNVLELWY ASA GSAADN PISQIAPDGF PDMSFVPFSG ITIPTAGWVG FGGIWNSSNG APYVTTMQAY ELGFATGVPS NPQPTTTTSG AQIV AKSIY GVANGINQTT AGLFVMASGV ISTPNSSATT YTPQPNRIVN APGTPAAAPI GKNTPIMFAS VVRRTGDINA EAGST NGTQ YGAGSQPLPV TIGLSLNNYS SALMPGQFFV WQLNFASGFM ELGLSVDGYF YAGTGASATL IDLSDLVDIR PVGPRP STS TLVYNLGGTT NGFSYV

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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 430 / Average exposure time: 3.26 sec. / Average electron dose: 24.87 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: 75000
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

Particle selectionNumber selected: 23888
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 18719
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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