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- EMDB-8598: The structure of human bocavirus 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-8598
TitleThe structure of human bocavirus 1
Map dataHuman bocavirus 1 (VP2 expressed in Sf9 cells using recombinant baculoviruses)
Samplehuman bocavirus 1 != Human bocavirus 1

human bocavirus 1

  • Virus: Human bocavirus 1
    • Protein or peptide: viral protein 3
KeywordsHBoV1 / human parvovirus 1 / parvovirus / respiratory tract infection / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 / phospholipase A2 activity / T=1 icosahedral viral capsid / lipid catabolic process / viral capsid / host cell cytoplasm / host cell nucleus / structural molecule activity
Similarity search - Function
Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Minor capsid protein VP1 / Minor capsid protein VP1
Similarity search - Component
Biological speciesHuman bocavirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMietzsch M / Kailasan S
CitationJournal: J Virol / Year: 2017
Title: Structural Insights into Human Bocaparvoviruses.
Authors: Mario Mietzsch / Shweta Kailasan / Jamie Garrison / Maria Ilyas / Paul Chipman / Kalle Kantola / Mandy E Janssen / John Spear / Duncan Sousa / Robert McKenna / Kevin Brown / Maria Söderlund- ...Authors: Mario Mietzsch / Shweta Kailasan / Jamie Garrison / Maria Ilyas / Paul Chipman / Kalle Kantola / Mandy E Janssen / John Spear / Duncan Sousa / Robert McKenna / Kevin Brown / Maria Söderlund-Venermo / Timothy Baker / Mavis Agbandje-McKenna /
Abstract: Bocaparvoviruses are emerging pathogens of the family. Human bocavirus 1 (HBoV1) causes severe respiratory infections and HBoV2 to HBoV4 cause gastrointestinal infections in young children. Recent ...Bocaparvoviruses are emerging pathogens of the family. Human bocavirus 1 (HBoV1) causes severe respiratory infections and HBoV2 to HBoV4 cause gastrointestinal infections in young children. Recent reports of life-threatening cases, lack of direct treatment or vaccination, and a limited understanding of their disease mechanisms highlight the need to study these pathogens on a molecular and structural level for the development of therapeutics. Toward this end, the capsid structures of HBoV1, HBoV3, and HBoV4 were determined to a resolution of 2.8 to 3.0 Å by cryo-electron microscopy and three-dimensional image reconstruction. The bocaparvovirus capsids, which display different tissue tropisms, have features in common with other parvoviruses, such as depressions at the icosahedral 2-fold symmetry axis and surrounding the 5-fold symmetry axis, protrusions surrounding the 3-fold symmetry axis, and a channel at the 5-fold symmetry axis. However, unlike other parvoviruses, densities extending the 5-fold channel into the capsid interior are conserved among the bocaparvoviruses and are suggestive of a genus-specific function. Additionally, their major viral protein 3 contains loops with variable regions at their apexes conferring capsid surface topologies different from those of other parvoviruses. Structural comparisons at the strain (HBoV) and genus (bovine parvovirus and HBoV) levels identified differences in surface loops that are functionally important in host/tissue tropism, pathogenicity, and antigenicity in other parvoviruses and likely play similar roles in these viruses. This study thus provides a structural framework to characterize determinants of host/tissue tropism, pathogenicity, and antigenicity for the development of antiviral strategies to control human bocavirus infections. Human bocaviruses are one of only a few members of the family pathogenic to humans, especially young children and immunocompromised adults. There are currently no treatments or vaccines for these viruses or the related enteric bocaviruses. This study obtained the first high-resolution structures of three human bocaparvoviruses determined by cryo-reconstruction. HBoV1 infects the respiratory tract, and HBoV3 and HBoV4 infect the gastrointestinal tract, tissues that are likely targeted by the capsid. Comparison of these viruses provides information on conserved bocaparvovirus-specific features and variable regions resulting in unique surface topologies that can serve as guides to characterize HBoV determinants of tissue tropism and antigenicity in future experiments. Based on the comparison to other existing parvovirus capsid structures, this study suggests capsid regions that likely control successful infection, including determinants of receptor attachment, host cell trafficking, and antigenic reactivity. Overall, these observations could impact efforts to design antiviral strategies and vaccines for HBoVs.
History
DepositionFeb 10, 2017-
Header (metadata) releaseMar 8, 2017-
Map releaseMar 29, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5urf
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5urf
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8598.map.gz / Format: CCP4 / Size: 242.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman bocavirus 1 (VP2 expressed in Sf9 cells using recombinant baculoviruses)
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-8.902677000000001 - 17.984793
Average (Standard dev.)-0.000000003019113 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-199-199-199
Dimensions399399399
Spacing399399399
CellA=B=C: 379.05 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.950.950.95
M x/y/z399399399
origin x/y/z0.0000.0000.000
length x/y/z379.050379.050379.050
α/β/γ90.00090.00090.000
start NX/NY/NZ-199-199-199
NX/NY/NZ399399399
MAP C/R/S213
start NC/NR/NS-199-199-199
NC/NR/NS399399399
D min/max/mean-8.90317.985-0.000

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Supplemental data

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Sample components

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Entire : human bocavirus 1

EntireName: human bocavirus 1
Components
  • Virus: Human bocavirus 1
    • Protein or peptide: viral protein 3

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Supramolecule #1: Human bocavirus 1

SupramoleculeName: Human bocavirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 689403 / Sci species name: Human bocavirus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: viral protein 3

MacromoleculeName: viral protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Human bocavirus 1
Molecular weightTheoretical: 60.568301 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDTDIQDQQ PDTVDAPQNT SGGGTGSIGG GKGSGVGIST GGWVGGSHFS DKYVVTKNTR QFITTIQNGH LYKTEAIETT NQSGKSQRC VTTPWTYFNF NQYSCHFSPQ DWQRLTNEYK RFRPKAMQVK IYNLQIKQIL SNGADTTYNN DLTAGVHIFC D GEHAYPNA ...String:
MSDTDIQDQQ PDTVDAPQNT SGGGTGSIGG GKGSGVGIST GGWVGGSHFS DKYVVTKNTR QFITTIQNGH LYKTEAIETT NQSGKSQRC VTTPWTYFNF NQYSCHFSPQ DWQRLTNEYK RFRPKAMQVK IYNLQIKQIL SNGADTTYNN DLTAGVHIFC D GEHAYPNA SHPWDEDVMP DLPYKTWKLF QYGYIPIENE LADLDGNAAG GNATEKALLY QMPFFLLENS DHQVLRTGES TE FTFNFDC EWVNNERAYI PPGLMFNPKV PTRRVQYIRQ NGSTAASTGR IQPYSKPTSW MTGPGLLSAQ RVGPQSSDTA PFM VCTNPE GTHINTGAAG FGSGFDPPSG CLAPTNLEYK LQWYQTPEGT GNNGNIIANP SLSMLRDQLL YKGNQTTYNL VGDI WMFPN QVWDRFPITR ENPIWCKKPR ADKHTIMDPF DGSIAMDHPP GTIFIKMAKI PVPTASNADS YLNIYCTGQV SCEIV WEVE RYATKNWRPE RRHTALGMSL GGESNYTPTY HVDPTGAYIQ PTSYDQCMPV KTNINKVL

UniProtKB: Minor capsid protein VP1

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 63.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31064
FSC plot (resolution estimation)

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