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- EMDB-8605: Human Bocavirus 4 -

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Basic information

Entry
Database: EMDB / ID: EMD-8605
TitleHuman Bocavirus 4Bocaparvovirus
Map dataHuman Bocavirus 4Bocaparvovirus
Sample
  • Virus: Human bocavirus 4
    • Protein or peptide: Capsid protein VP2
KeywordsHuman bocavirus 4 / Parvovirus / gastroenteritis / 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 / 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 4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMietzsch M / Agbandje-McKenna M
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 13, 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 with section colored by density value
  • 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-5us9
  • Surface level: 1
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5us9
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Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8605.map.gz / Format: CCP4 / Size: 242.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Bocavirus 4
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-8.80025 - 16.946280000000002
Average (Standard dev.)0.000000000721446 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
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/NZ000
NX/NY/NZ399399399
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS399399399
D min/max/mean-8.80016.9460.000

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Supplemental data

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Sample components

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Entire : Human bocavirus 4

EntireName: Human bocavirus 4
Components
  • Virus: Human bocavirus 4
    • Protein or peptide: Capsid protein VP2

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Supramolecule #1: Human bocavirus 4

SupramoleculeName: Human bocavirus 4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 645161 / Sci species name: Human bocavirus 4 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Human bocavirus 4
Molecular weightTheoretical: 61.033809 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSENEIQDQQ PSDSMDGQRG GGGGATGSVG GGKGSGVGIS TGGWVGGSYF TDSYVITKNT RQFLVKIQNN HQYKTELISP STSQGKSQR CVSTPWSYFN FNQYSSHFSP QDWQRLTNEY KRFRPKGMHV KIYNLQIKQI LSNGADTTYN NDLTAGVHIF C DGEHAYPN ...String:
MSENEIQDQQ PSDSMDGQRG GGGGATGSVG GGKGSGVGIS TGGWVGGSYF TDSYVITKNT RQFLVKIQNN HQYKTELISP STSQGKSQR CVSTPWSYFN FNQYSSHFSP QDWQRLTNEY KRFRPKGMHV KIYNLQIKQI LSNGADTTYN NDLTAGVHIF C DGEHAYPN ATHPWDEDVM PELPYQTWYL FQYGYIPVIH ELAEMEDSNA VEKAICLQIP FFMLENSDHE VLRTGESTEF TF NFDCEWI NNERAYIPPG LMFNPLVPTR RAQYIRRNNN PQTAESTSRI APYAKPTSWM TGPGLLSAQR VGPATSDTGA WMV AVKPEN ASIDTGMSGI GSGFDPPQGS LAPTNLEYKI QWYQTPQGTN NNGNIISNQP LSMLRDQALF RGNQTTYNLC SDVW MFPNQ IWDRYPITRE NPIWCKKPRS DKHTTIDPFD GSLAMDHPPG TIFIKMAKIP VPSNNNADSY LNIYCTGQVS CEIVW EVER YATKNWRPER RHTTFGLGIG GADNLNPTYH VDKNGTYIQP TTWDMCFPVK TNINKVL

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: 60.0 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13394

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