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- PDB-7l0y: Human Bocavirus 1 (pH 2.6) -

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Basic information

Entry
Database: PDB / ID: 7l0y
TitleHuman Bocavirus 1 (pH 2.6)
ComponentsVP2
KeywordsVIRUS / Icosahedral Capsid / Human Bocavirus 1 / HBoV1 / Parvovirus
Function / homologyParvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / VP2
Function and homology information
Biological speciesPrimate bocaparvovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsLuo, M. / Mietzsch, M. / Agbandje-McKenna, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: J Virol / Year: 2021
Title: pH-Induced Conformational Changes of Human Bocavirus Capsids.
Authors: Mengxiao Luo / Mario Mietzsch / Paul Chipman / Kangkang Song / Chen Xu / John Spear / Duncan Sousa / Robert McKenna / Maria Söderlund-Venermo / Mavis Agbandje-McKenna /
Abstract: Human bocavirus 1 (HBoV1) and HBoV2-4 infect children and immunocompromised individuals, resulting in respiratory and gastrointestinal infections, respectively. Using cryo-electron microscopy and ...Human bocavirus 1 (HBoV1) and HBoV2-4 infect children and immunocompromised individuals, resulting in respiratory and gastrointestinal infections, respectively. Using cryo-electron microscopy and image reconstruction, the HBoV2 capsid structure was determined to 2.7 Å resolution at pH 7.4 and compared to the previously determined HBoV1, HBoV3, and HBoV4 structures. Consistent with previous findings, surface variable region (VR) III of the capsid protein VP3, proposed as a host tissue-tropism determinant, was structurally similar among the gastrointestinal strains HBoV2-4, but differed from HBoV1 with its tropism for the respiratory tract. Towards understanding the entry and trafficking properties of these viruses, HBoV1 and HBoV2 were further analyzed as species representatives of the two HBoV tropisms. Their cell surface glycan-binding characteristics were analyzed, and capsid structures determined to 2.5-2.7 Å resolution at pH 5.5 and 2.6, conditions normally encountered during infection. The data showed that glycans with terminal sialic acid, galactose, GlcNAc or heparan sulfate moieties do not facilitate HBoV1 or HBoV2 cellular attachment. With respect to trafficking, conformational changes common to both viruses were observed at low pH conditions localized to the VP N-terminus under the 5-fold channel, in the surface loops VR-I and VR-V and specific side-chain residues such as cysteines and histidines. The 5-fold conformational movements provide insight into the potential mechanism of VP N-terminal dynamics during HBoV infection and side-chain modifications highlight pH-sensitive regions of the capsid. Human bocaviruses (HBoVs) are associated with disease in humans. However, the lack of an animal model and a versatile cell culture system to study their life cycle limits the ability to develop specific treatments or vaccines. This study presents the structure of HBoV2, at 2.7 Å resolution, determined for comparison to the existing HBoV1, HBoV3, and HBoV4 structures, to enable the molecular characterization of strain and genus-specific capsid features contributing to tissue tropism and antigenicity. Furthermore, HBoV1 and HBoV2 structures determined under acidic conditions provide insight into capsid changes associated with endosomal and gastrointestinal acidification. Structural rearrangements of the capsid VP N-terminus, at the base of the 5-fold channel, demonstrate a disordering of a "basket" motif as pH decreases. These observations begin to unravel the molecular mechanism of HBoV infection and provide information for control strategies.
History
DepositionDec 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: VP2
B: VP2
C: VP2
D: VP2
E: VP2
F: VP2
G: VP2
H: VP2
I: VP2
J: VP2
K: VP2
L: VP2
M: VP2
N: VP2
O: VP2
P: VP2
Q: VP2
R: VP2
S: VP2
T: VP2
U: VP2
V: VP2
W: VP2
X: VP2
Y: VP2
Z: VP2
a: VP2
b: VP2
c: VP2
d: VP2
e: VP2
f: VP2
g: VP2
h: VP2
i: VP2
j: VP2
k: VP2
l: VP2
m: VP2
n: VP2
o: VP2
p: VP2
q: VP2
r: VP2
s: VP2
t: VP2
u: VP2
v: VP2
w: VP2
x: VP2
y: VP2
z: VP2
1: VP2
2: VP2
3: VP2
4: VP2
5: VP2
6: VP2
7: VP2
8: VP2


Theoretical massNumber of molelcules
Total (without water)3,489,95260
Polymers3,489,95260
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
VP2


Mass: 58165.867 Da / Num. of mol.: 60 / Fragment: UNP residues 24-542
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Primate bocaparvovirus 1 (strain Human bocavirus 1 type 1)
Strain: Human bocavirus 1 type 1 / Gene: vp2, VP2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: H9C5X6

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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 1Bocaparvovirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human bocavirus 1
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 5.5
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 FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10-2155_2155: / Classification: refinement
EM software
IDNameCategory
4cisTEMCTF correction
13cisTEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50342 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01253080
ELECTRON MICROSCOPYf_angle_d0.851345060
ELECTRON MICROSCOPYf_dihedral_angle_d9.01202020
ELECTRON MICROSCOPYf_chiral_restr0.0636060
ELECTRON MICROSCOPYf_plane_restr0.00745480

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