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- PDB-9cv9: Bufavirus 1 at pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 9cv9
TitleBufavirus 1 at pH 4.0
ComponentsVP1
KeywordsVIRUS LIKE PARTICLE / Bufavirus / parvovirus
Function / homologyPhospholipase 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 / T=1 icosahedral viral capsid / structural molecule activity / VP1
Function and homology information
Biological speciesBufavirus-1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGulkis, M.C. / McKenna, R. / Bennett, A.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: Viruses / Year: 2024
Title: Structural Characterization of Human Bufavirus 1: Receptor Binding and Endosomal pH-Induced Changes.
Authors: Mitchell Gulkis / Mengxiao Luo / Paul Chipman / Mario Mietzsch / Maria Söderlund-Venermo / Antonette Bennett / Robert McKenna /
Abstract: Bufaviruses (BuV) are members of the of the genus. They are non-enveloped, T = 1 icosahedral ssDNA viruses isolated from patients exhibiting acute diarrhea. The lack of treatment options and a ...Bufaviruses (BuV) are members of the of the genus. They are non-enveloped, T = 1 icosahedral ssDNA viruses isolated from patients exhibiting acute diarrhea. The lack of treatment options and a limited understanding of their disease mechanisms require studying these viruses on a molecular and structural level. In the present study, we utilize glycan arrays and cell binding assays to demonstrate that BuV1 capsid binds terminal sialic acid (SIA) glycans. Furthermore, using cryo-electron microscopy (cryo-EM), SIA is shown to bind on the 2/5-fold wall of the capsid surface. Interestingly, the capsid residues stabilizing SIA binding are conserved in all human BuVs identified to date. Additionally, biophysical assays illustrate BuV1 capsid stabilization during endo-lysosomal (pH 7.4-pH 4) trafficking and capsid destabilization at pH 3 and less, which correspond to the pH of the stomach. Hence, we determined the cryo-EM structures of BuV1 capsids at pH 7.4, 4.0, and 2.6 to 2.8 Å, 3.2 Å, and 2.7 Å, respectively. These structures reveal capsid structural rearrangements during endo-lysosomal escape and provide a potential mechanism for this process. The structural insights gained from this study will add to the general knowledge of human pathogenic parvoviruses. Furthermore, the identification of the conserved SIA receptor binding site among BuVs provides a possible targetable surface-accessible pocket for the design of small molecules to be developed as anti-virals for these viruses.
History
DepositionJul 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Sep 18, 2024Group: Data collection / Database references / Category: citation_author / em_admin
Item: _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
K: VP1
L: VP1
M: VP1
N: VP1
O: VP1
P: VP1
Q: VP1
R: VP1
S: VP1
T: VP1
U: VP1
V: VP1
W: VP1
X: VP1
Y: VP1
Z: VP1
a: VP1
b: VP1
c: VP1
d: VP1
e: VP1
f: VP1
g: VP1
h: VP1
i: VP1
j: VP1
k: VP1
l: VP1
m: VP1
n: VP1
o: VP1
p: VP1
q: VP1
r: VP1
s: VP1
t: VP1
u: VP1
v: VP1
w: VP1
x: VP1
y: VP1
z: VP1
1: VP1
2: VP1
3: VP1
4: VP1
5: VP1
6: VP1
7: VP1
8: VP1


Theoretical massNumber of molelcules
Total (without water)4,832,59260
Polymers4,832,59260
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
VP1


Mass: 80543.203 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bufavirus-1 / Gene: BF-002 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A097PIM0

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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: Bufavirus-1 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 4 MDa / Experimental value: NO
Source (natural)Organism: Bufavirus-1
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf9
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 260 nm / Triangulation number (T number): 1
Buffer solutionpH: 4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
220 mMMESC6H13NO4S1
320 mMSodium AcetateCH3COONa1
4150 mMSodium ChlorideNaCl1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 100 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 75 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 827
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 50 / Used frames/image: 1-50

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2Leginonimage acquisition
4cryoSPARC4.4.1CTF correction
7UCSF Chimeramodel fitting
9cryoSPARC4.4.1initial Euler assignment
10cryoSPARC4.4.1final Euler assignment
11cryoSPARC4.4.1classification
12cryoSPARC4.4.13D reconstruction
13PHENIX1.10-2155_2155:model refinement
14Coot0.8.9.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 121209
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55060 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 174.8 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 6BWX

6bwx


Accession code: 6BWX / Source name: PDB / Type: experimental model

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