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- EMDB-52593: Capsid of RHDV mutant - N15 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52593
TitleCapsid of RHDV mutant - N15
Map dataSharpened map of RHDV mutant N15
Sample
  • Virus: Rabbit hemorrhagic disease virus
    • Protein or peptide: Capsid protein VP60
    • Protein or peptide: Capsid protein VP60
    • Protein or peptide: Three-fold helix
KeywordsCalicivirus / cryoEM / VLP / Assembly / VIRUS LIKE PARTICLE
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-AST89 / Oryctolagus cuniculus (rabbit) / Rabbit hemorrhagic disease virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 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 RHDV mutant N15 at 2.5 Angstroms resolution
Authors: Novoa G / Martinez-Romero JM / Perez-Mata C / Barcena J / Caston JR
History
DepositionJan 23, 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_52593.png

Downloads & links

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Map

FileDownload / File: emd_52593.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of RHDV mutant N15
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 440 pix.
= 475.2 Å		1.08 Å/pix.
x 440 pix.
= 475.2 Å		1.08 Å/pix.
x 440 pix.
= 475.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-3.7616882 - 6.794045
Average (Standard dev.)0.03866881 (±0.3902236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 475.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of RHDV mutant N15

Fileemd_52593_additional_1.map
AnnotationUnsharpened map of RHDV mutant N15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of RHDV mutant N15

Fileemd_52593_half_map_1.map
AnnotationHalf map B of RHDV mutant N15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of RHDV mutant N15

Fileemd_52593_half_map_2.map
AnnotationHalf map A of RHDV mutant N15
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
    • Protein or peptide: Capsid protein VP60
    • Protein or peptide: Three-fold helix

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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
Virus shellShell ID: 1 / Diameter: 410.0 Å

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Macromolecule #1: Capsid protein VP60

MacromoleculeName: Capsid protein VP60 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rabbit hemorrhagic disease virus-AST89
Molecular weightTheoretical: 57.526844 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SVPGTTTDGM DPGVVATTSV VTAENSSASI ATAGIGGPPQ QVDQQETWRT NFYYNDVFTW SVADAPGSIL YTVQHSPQNN PFTAVLSQM YAGWAGGMQF RFIVAGSGVF GGRLVAAVIP PGIEIGPGLE VRQFPHVVID ARSLEPVTIT MPDLRPNMYH P TGDPGLVP ...String:
SVPGTTTDGM DPGVVATTSV VTAENSSASI ATAGIGGPPQ QVDQQETWRT NFYYNDVFTW SVADAPGSIL YTVQHSPQNN PFTAVLSQM YAGWAGGMQF RFIVAGSGVF GGRLVAAVIP PGIEIGPGLE VRQFPHVVID ARSLEPVTIT MPDLRPNMYH P TGDPGLVP TLVLSVYNNL INPFGGSTSA IQVTVETRPS EDFEFVMIRA PSSKTVDSIS PAGLLTTPVL TGVGNDNRWN GQ IVGLQPV PGGFSTCNRH WNLNGSTYGW SSPRFADIDH RRGSASYPGN NATNVLQFWY ANAGSAIDNP ISQVAPDGFP DMS FVPFNG PGIPAAGWVG FGAIWNSNSG APNVTTVQAY ELGFATGAPG NLQPTTNTSG SQTVAKSIYA VVTGTAQNPA GLFV MASGV ISTPSANAIT YTPQPDRIVT TPGTPAAAPV GKNTPIMFAS VVRRTGDVNA TAGSANGTQY GTGSQPLPVT IGLSL NNYS SALMPGQFFV WQLTFASGFM EIGLSVDGYF YAGTGASTTL IDLTELIDVR PVGPRPSKST LVFNLGG

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP60

MacromoleculeName: Capsid protein VP60 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rabbit hemorrhagic disease virus-AST89
Molecular weightTheoretical: 57.51282 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SVPGTTTDGM DPGVVATTSV VTAENSSASV ATAGIGGPPQ QVDQQETWRT NFYYNDVFTW SVADAPGSIL YTVQHSPQNN PFTAVLSQM YAGWAGGMQF RFIVAGSGVF GGRLVAAVIP PGIEIGPGLE VRQFPHVVID ARSLEPVTIT MPDLRPNMYH P TGDPGLVP ...String:
SVPGTTTDGM DPGVVATTSV VTAENSSASV ATAGIGGPPQ QVDQQETWRT NFYYNDVFTW SVADAPGSIL YTVQHSPQNN PFTAVLSQM YAGWAGGMQF RFIVAGSGVF GGRLVAAVIP PGIEIGPGLE VRQFPHVVID ARSLEPVTIT MPDLRPNMYH P TGDPGLVP TLVLSVYNNL INPFGGSTSA IQVTVETRPS EDFEFVMIRA PSSKTVDSIS PAGLLTTPVL TGVGNDNRWN GQ IVGLQPV PGGFSTCNRH WNLNGSTYGW SSPRFADIDH RRGSASYPGN NATNVLQFWY ANAGSAIDNP ISQVAPDGFP DMS FVPFNG PGIPAAGWVG FGAIWNSNSG APNVTTVQAY ELGFATGAPG NLQPTTNTSG SQTVAKSIYA VVTGTAQNPA GLFV MASGV ISTPSANAIT YTPQPDRIVT TPGTPAAAPV GKNTPIMFAS VVRRTGDVNA TAGSANGTQY GTGSQPLPVT IGLSL NNYS SALMPGQFFV WQLTFASGFM EIGLSVDGYF YAGTGASTTL IDLTELIDVR PVGPRPSKST LVFNLGG

UniProtKB: Genome polyprotein

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Macromolecule #3: Three-fold helix

MacromoleculeName: Three-fold helix / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 1.340437 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
AAEFFEGMVH DS

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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: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 32.0 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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50616
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9i3h:
CP of RHDV mutant - N15

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