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- EMDB-52757: Capsid of RHDV virion (full particle) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52757
TitleCapsid of RHDV virion (full particle)
Map dataUnsharpened map of RHDV virion
Sample
  • Virus: Rabbit hemorrhagic disease virus
    • Protein or peptide: Capsid protein VP60
KeywordsCalicivirus / cryoEM / virion / Assembly / VIRUS
Function / homology
Function and homology information


calicivirin / host cell endoplasmic reticulum / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity ...calicivirin / host cell endoplasmic reticulum / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding
Similarity search - Function
: / Viral genome-linked protein / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. ...: / Viral genome-linked protein / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit) / Rabbit hemorrhagic disease virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsNovoa G / Martinez-Romero JM / Perez-Mata C / Barcena J / Caston JR
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2023-146143NB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-140925OB-I00 Spain
CitationJournal: To Be Published
Title: Structure of full RHDV virion at 3.3 Angstroms resolution
Authors: Novoa G / Martinez-Romero JM / Perez-Mata C / Barcena J / Caston JR
History
DepositionFeb 6, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52757.png

Downloads & links

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Map

FileDownload / File: emd_52757.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map of RHDV virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 330 pix.
= 452.1 Å		1.37 Å/pix.
x 330 pix.
= 452.1 Å		1.37 Å/pix.
x 330 pix.
= 452.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-3.193722 - 6.78487
Average (Standard dev.)0.08036766 (±0.43438825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 452.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of RHDV virion

Fileemd_52757_additional_1.map
AnnotationUnsharpened map of RHDV virion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A map of RHDV virion

Fileemd_52757_half_map_1.map
AnnotationHalf A map of RHDV virion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B map of RHDV virion

Fileemd_52757_half_map_2.map
AnnotationHalf B map of RHDV virion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rabbit hemorrhagic disease virus

EntireName: Rabbit hemorrhagic disease virus
Components
  • Virus: Rabbit hemorrhagic disease virus
    • Protein or peptide: Capsid protein VP60

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Supramolecule #1: Rabbit hemorrhagic disease virus

SupramoleculeName: Rabbit hemorrhagic disease virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 11976 / Sci species name: Rabbit hemorrhagic disease virus / Virus type: VIRION / Virus isolate: OTHER / 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 VP60

MacromoleculeName: Capsid protein VP60 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 60.00952 KDa
SequenceString: GKARTAPQGE AAGTATTASV PGTTTDGMDP GVVATTSVVT AENSSASIAT AGIGGPPQQV DQQETWRTNF YYNDVFTWSV ADAPGSILY TVQHSPQNNP FTAVLSQMYA GWAGGMQFRF IVAGSGVFGG RLVAAVIPPG IEIGPGLEVR QFPHVVIDAR S LEPVTITM ...String:
GKARTAPQGE AAGTATTASV PGTTTDGMDP GVVATTSVVT AENSSASIAT AGIGGPPQQV DQQETWRTNF YYNDVFTWSV ADAPGSILY TVQHSPQNNP FTAVLSQMYA GWAGGMQFRF IVAGSGVFGG RLVAAVIPPG IEIGPGLEVR QFPHVVIDAR S LEPVTITM PDLRPNMYHP TGDPGLVPTL VLSVYNNLIN PFGGSTSAIQ VTVETRPSED FEFVMIRAPS SKTVDSISPA GL LTTPVLT GVGNDNRWNG QIVGLQPVPG GFSTCNRHWN LNGSTYGWSS PRFADIDHRR GSASYPGNNA TNVLQFWYAN AGS AIDNPI SQVAPDGFPD MSFVPFNGPG IPAAGWVGFG AIWNSNSGAP NVTTVQAYEL GFATGAPGNL QPTTNTSGSQ TVAK SIYAV VTGTAQNPAG LFVMASGVIS TPSANAITYT PQPDRIVTTP GTPAAAPVGK NTPIMFASVV RRTGDVNATA GSANG TQYG TGSQPLPVTI GLSLNNYSSA LMPGQFFVWQ LTFASGFMEI GLSVDGYFYA GTGASTTLID LTELIDVRPV GPRPSK STL VFNLGGTANG FSYV

UniProtKB: Genome polyprotein

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 2824 / Average electron dose: 29.7 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25237
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9i9d:
CP of RHDV virion (full particle)

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