[English] 日本語
Yorodumi
- EMDB-41615: The Capsid of Porcine Bocavirus 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41615
TitleThe Capsid of Porcine Bocavirus 1
Map data
Sample
  • Virus: Porcine bocavirus 1 pig/ZJD/China/2006
    • Protein or peptide: VP2
KeywordsParvovirus / PBoV1 / Porcine 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 speciesPorcine bocavirus 1 pig/ZJD/China/2006
Methodsingle particle reconstruction / cryo EM / Resolution: 2.31 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

-
Structure visualization

Supplemental images

emd_41615.png

Downloads & links

-
Map

FileDownload / File: emd_41615.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.91 Å/pix.
x 420 pix.
= 383.46 Å		0.91 Å/pix.
x 420 pix.
= 383.46 Å		0.91 Å/pix.
x 420 pix.
= 383.46 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.913 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-9.059324 - 18.414400000000001
Average (Standard dev.)-0.00000000253555 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 383.46 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_41615_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41615_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Porcine bocavirus 1 pig/ZJD/China/2006

EntireName: Porcine bocavirus 1 pig/ZJD/China/2006
Components
  • Virus: Porcine bocavirus 1 pig/ZJD/China/2006
    • Protein or peptide: VP2

-
Supramolecule #1: Porcine bocavirus 1 pig/ZJD/China/2006

SupramoleculeName: Porcine bocavirus 1 pig/ZJD/China/2006 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 795694 / Sci species name: Porcine bocavirus 1 pig/ZJD/China/2006 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

-
Macromolecule #1: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Porcine bocavirus 1 pig/ZJD/China/2006
Molecular weightTheoretical: 63.370266 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSGGDPSED TGAGDGEQGG ESSAMAGRSG GGMGGGGGGG GSVGFSTGGW EGGTYFSDHT VTTTNTRQWY TGILNGHRYS KLAQTTGSN LQAAKPWVGI QTPWAYLNLN CYHCHFSPQD WQRLLNEYKA WRPKRMHVRI YNLQIKQITT VGADTLYQND L TAGVHIFC ...String:
MSSGGDPSED TGAGDGEQGG ESSAMAGRSG GGMGGGGGGG GSVGFSTGGW EGGTYFSDHT VTTTNTRQWY TGILNGHRYS KLAQTTGSN LQAAKPWVGI QTPWAYLNLN CYHCHFSPQD WQRLLNEYKA WRPKRMHVRI YNLQIKQITT VGADTLYQND L TAGVHIFC DGSHQYPYAQ HPWDEGASPE LPNEIWKLPQ YAYFQYQGDL TDHATANTPQ NVESMLRSNI PLFLLENSNH EV LRTGEMT EFSFTFQSGW VTNDRAYCCP QSDFNPLVQT RRYYPTWNGS SNSYSYNRYG PYKKPSNWMP GPGLAYKGAT HTN QNPDDA RGPIVTTIAP RGTISVGSTP SNDAPNDGDN TISSDGVKQG GWQTAPVNGA CSRTDYPTLA FDPSDRSTNQ NIPT RNLDI DMTRWYRVHE PVRSGNGSTY YNVDDVWMYP NQVWNSTPIC RDNPIWDKVP RTDHHTLLDS SDGTLPMKHP PGNIF IKCA KIPIPTSNNT DSYLNIYVTG QVTYTVEWEV QRYQTKNWRP ELRTSAGTYN QHEIYNIGEN GTYNRANTFN ECMPTK CGI NRVL

UniProtKB: VP2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98388
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more