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- EMDB-52733: Capsid of RHDV VLP (VP1) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52733
TitleCapsid of RHDV VLP (VP1)
Map dataSharpened map of RHDV VLP (VP1).
Sample
  • Virus: Rabbit hemorrhagic disease virus
    • Protein or peptide: Capsid protein VP60
KeywordsCalicivirus / Localized reconstruction / CryoEM / Virus Like Particle / VIRAL PROTEIN
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 speciesRabbit 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 UniversitiesPID2023-146132NB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-140925OB-I00 Spain
CitationJournal: To Be Published
Title: CP of RHDV VLP (VP1)
Authors: Novoa G / Martinez-Romero JM / Perez-Mata C / Barcena J / Caston JR
History
DepositionFeb 5, 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_52733.png

Downloads & links

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Map

FileDownload / File: emd_52733.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of RHDV VLP (VP1).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 440 pix.
= 466.4 Å		1.06 Å/pix.
x 440 pix.
= 466.4 Å		1.06 Å/pix.
x 440 pix.
= 466.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.47
Minimum - Maximum-1.1360692 - 2.2065287
Average (Standard dev.)0.0074972874 (±0.17651966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 466.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of RHDV VLP (VP1).

Fileemd_52733_additional_1.map
AnnotationUnsharpened map of RHDV VLP (VP1).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of RHDV VLP (VP1).

Fileemd_52733_half_map_1.map
AnnotationHalf map A of RHDV VLP (VP1).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of RHDV VLP (VP1).

Fileemd_52733_half_map_2.map
AnnotationHalf map B of RHDV VLP (VP1).
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: all / NCBI-ID: 11976 / Sci species name: Rabbit hemorrhagic disease virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Oryctolagus cuniculus (rabbit)

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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: Rabbit hemorrhagic disease virus
Molecular weightTheoretical: 60.00952 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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: 43950
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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