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- EMDB-41616: The Capsid of Rat Bocavirus -

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Basic information

Entry
Database: EMDB / ID: EMD-41616
TitleThe Capsid of Rat Bocavirus
Map data
Sample
  • Virus: Rat bocavirus
    • Protein or peptide: VP2
KeywordsParvovirus / RBoV / Rat Bocavirus / Capsid / VIRUS
Function / homologyParvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / VP2
Function and homology information
Biological speciesRat bocavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsVelez M / Mietzsch M / McKenna R / Afione S / Zeher A / Huang R / Chiorini J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: Viruses / Year: 2023
Title: Structural Characterization of Canine Minute Virus, Rat and Porcine Bocavirus.
Authors: Michael Velez / Mario Mietzsch / Jane Hsi / Logan Bell / Paul Chipman / Xiaofeng Fu / Robert McKenna /
Abstract: is an expansive genus of the , with a wide range of vertebrate hosts. This study investigates Canine minute virus (CnMV), Rat bocavirus (RBoV), and Porcine bocavirus 1 (PBoV1). Both CnMV and PBoV1 ... is an expansive genus of the , with a wide range of vertebrate hosts. This study investigates Canine minute virus (CnMV), Rat bocavirus (RBoV), and Porcine bocavirus 1 (PBoV1). Both CnMV and PBoV1 have been found in gastrointestinal infections in their respective hosts, with CnMV responsible for spontaneous abortions in dogs, while PBoV has been associated with encephalomyelitis in piglets. The pathogenicity of the recently identified RBoV is currently unknown. To initiate the characterization of these viruses, their capsids structures were determined by cryo-electron microscopy at resolutions ranging from 2.3 to 2.7 Å. Compared to other parvoviruses, the CnMV, PBoV1, and RBoV capsids showed conserved features, such as the channel at the fivefold symmetry axis. However, major differences were observed at the two- and threefold axes. While CnMV displays prominent threefold protrusions, the same region is more recessed in PBoV1 and RBoV. Furthermore, the typical twofold axis depression of parvoviral capsids is absent in CnMV or very small in PBoV and RBoV. These capsid structures extend the structural portfolio for the genus and will allow future characterization of these pathogens on a molecular level. This is important, as no antivirals or vaccines exist for these viruses.
History
DepositionAug 15, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41616.png

Downloads & links

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Map

FileDownload / File: emd_41616.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.92 Å/pix.
x 420 pix.
= 386.82 Å		0.92 Å/pix.
x 420 pix.
= 386.82 Å		0.92 Å/pix.
x 420 pix.
= 386.82 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.921 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-8.411282 - 16.707965999999999
Average (Standard dev.)0.00000000180623 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 386.82 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41616_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41616_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Rat bocavirus

EntireName: Rat bocavirus
Components
  • Virus: Rat bocavirus
    • Protein or peptide: VP2

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Supramolecule #1: Rat bocavirus

SupramoleculeName: Rat bocavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1788315 / Sci species name: Rat bocavirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Rat bocavirus
Molecular weightTheoretical: 63.540734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADGGESSNA NAGEGTSGGG GSGPLALTGG SRAGGTIGGG GAGSVGFSTG GWTAGTYFSD NKVVTNQTRQ FLTPIYNGHT YKALQADDL TNENDKSKWN GITTPWGYFN FNCYASHFSP QDWQRMCNEY KRWRPKRLRV QIYNLQLKTI QSNGADTQYN N DLTAAVHI ...String:
MADGGESSNA NAGEGTSGGG GSGPLALTGG SRAGGTIGGG GAGSVGFSTG GWTAGTYFSD NKVVTNQTRQ FLTPIYNGHT YKALQADDL TNENDKSKWN GITTPWGYFN FNCYASHFSP QDWQRMCNEY KRWRPKRLRV QIYNLQLKTI QSNGADTQYN N DLTAAVHI LVDGSHQFPW AQHPWDDTCA PELPYVIYKT PQYAYFQNLA GLANNVGTNS ANKFLKMNTP LYVLETMSHE VL RTGEDTS FEFEMSSGWV DNQTNFCPPQ LDFNPLHDTR RVAPRATNNT TQYAPYPKFK KPSNWVPGPG MAYPGRGEAD GKR PAPMTV TLRPNTFIDA GNNTTDRFQQ ASYQEWKPTD DTIIGQSINV GPINCAATDP DAVTTAADAE DDVANPNTDK VSSH RYSID MTRWNAIQIN VRRNNGTPET TQIYRHYLYP MQAWNSNQID RYTPIWDKVP NTEWHTMLAS SDGTLPMTHP PGTIF IKCS KIPVPSENNA DSYLNIYCTG QVSYEIEWEC ERYNTKNWRP ELRVDPKNWT DPNNYNLNTQ GGYIVNEELY ETMPTK IGI NRVN

UniProtKB: VP2

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.4 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: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9199
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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