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- PDB-9cuz: Bufavirus 1 complexed with 6SLN -

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Basic information

Entry
Database: PDB / ID: 9cuz
TitleBufavirus 1 complexed with 6SLN
ComponentsVP1
KeywordsVIRUS LIKE PARTICLE / Bufavirus / parvovirus / glycan
Function / homology
Function and homology information


T=1 icosahedral viral capsid / 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
N-acetyl-alpha-neuraminic acid / VP1
Similarity search - Component
Biological speciesBufavirus-1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.16 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 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,851,148120
Polymers4,832,59260
Non-polymers18,55660
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
#2: Sugar...
ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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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 / Details: Bufavirus 1 VP2 was overexpressed in Sf9 cells / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 4 MDa / Experimental value: NO
Source (natural)Organism: Bufavirus-1
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
220 mMMESC6H13NO4S1
320 mMSodium AcetateCH3COONa1
4150 mMNaClNaCl1
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 defocus max: 3600 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: 1115
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 50 / Used frames/image: 1-50

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 250990
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95075 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 90.4 / 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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