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- PDB-5urf: The structure of human bocavirus 1 -

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Basic information

Entry
Database: PDB / ID: 5urf
TitleThe structure of human bocavirus 1
Componentsviral protein 3
KeywordsVIRUS LIKE PARTICLE / HBoV1 / human parvovirus 1 / parvovirus / respiratory tract infection
Function / homology
Function and homology information


phospholipase A2 activity / phospholipase A2 / 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 VP1/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
MethodELECTRON MICROSCOPY / single 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. ...Mietzsch, 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- ...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, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 29, 2017Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 14, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: viral protein 3
B: viral protein 3
C: viral protein 3
D: viral protein 3
E: viral protein 3
F: viral protein 3
G: viral protein 3
H: viral protein 3
I: viral protein 3
J: viral protein 3
K: viral protein 3
L: viral protein 3
M: viral protein 3
N: viral protein 3
O: viral protein 3
P: viral protein 3
Q: viral protein 3
R: viral protein 3
S: viral protein 3
T: viral protein 3
U: viral protein 3
V: viral protein 3
W: viral protein 3
X: viral protein 3
Y: viral protein 3
Z: viral protein 3
1: viral protein 3
2: viral protein 3
3: viral protein 3
4: viral protein 3
5: viral protein 3
6: viral protein 3
a: viral protein 3
b: viral protein 3
c: viral protein 3
d: viral protein 3
e: viral protein 3
f: viral protein 3
g: viral protein 3
h: viral protein 3
i: viral protein 3
j: viral protein 3
k: viral protein 3
l: viral protein 3
m: viral protein 3
n: viral protein 3
o: viral protein 3
p: viral protein 3
q: viral protein 3
r: viral protein 3
s: viral protein 3
t: viral protein 3
u: viral protein 3
v: viral protein 3
w: viral protein 3
x: viral protein 3
y: viral protein 3
z: viral protein 3
7: viral protein 3
8: viral protein 3


Theoretical massNumber of molelcules
Total (without water)3,634,09860
Polymers3,634,09860
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area850210 Å2
ΔGint-4516 kcal/mol
Surface area798460 Å2

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Components

#1: Protein ...
viral protein 3 / VP3 / VP1-VP2


Mass: 60568.301 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human bocavirus 1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: U5XGX2, UniProt: Q3YPH4*PLUS
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human bocavirus 1 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human bocavirus 1
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 63 e/Å2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)

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Processing

SoftwareName: PHENIX / Version: 1.10-2155_2155: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31064 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011251280
ELECTRON MICROSCOPYf_angle_d1.456343020
ELECTRON MICROSCOPYf_dihedral_angle_d8.308253740
ELECTRON MICROSCOPYf_chiral_restr0.07135820
ELECTRON MICROSCOPYf_plane_restr0.00945180

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