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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 data
Samplehuman bocavirus 1:
virus / viral protein 3
Function / homology
Function and homology information


T=1 icosahedral viral capsid / phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine) / phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine) / phospholipase A2 / phospholipase A2 activity / lipid catabolic process / viral capsid / host cell cytoplasm / host cell nucleus / structural molecule activity
Parvovirus coat protein VP2 / Parvovirus coat protein VP1 / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus / Parvovirus coat protein VP1, N-terminal
Minor capsid protein VP1 / Minor capsid protein VP1
Biological speciesHuman bocavirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMietzsch M / Kailasan S / Garrison J / Ilyas M / Chipman P / Kandola K / Jansen M / Spear J / Sousa D / McKenna R / Soderlund-Venermo M / Baker T / 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-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.
Validation ReportPDB-ID: 5urf

SummaryFull reportAbout validation report
DateDeposition: Feb 10, 2017 / Header (metadata) release: Mar 8, 2017 / Map release: Mar 29, 2017 / Update: May 24, 2017

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Structure visualization

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  • 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 models: PDB-5urf
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Structure viewerEM map:
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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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.95 Å/pix.
x 399 pix.
= 379.05 Å
0.95 Å/pix.
x 399 pix.
= 379.05 Å
0.95 Å/pix.
x 399 pix.
= 379.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 1. / Movie #1: 1
Minimum - Maximum-8.902677000000001 - 17.984793
Average (Standard dev.)-0.000000003019113 (±1.)
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 / Number of components: 2

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Component #1: virus, Human bocavirus 1

VirusName: Human bocavirus 1Bocaparvovirus / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: SEROTYPE
SpeciesSpecies: Human bocavirus 1
Source (natural)Host Species: Homo sapiens (human)

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Component #2: protein, viral protein 3

ProteinName: viral protein 3 / Number of Copies: 60 / Recombinant expression: No
MassTheoretical: 60.568301 kDa
SourceSpecies: Human bocavirus 1
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 63 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 31064
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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