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- PDB-6bwx: Atomic resolution structure of human bufavirus 1 -

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Basic information

Entry
Database: PDB / ID: 6bwx
TitleAtomic resolution structure of human bufavirus 1
ComponentsVP2
KeywordsVIRUS LIKE PARTICLE / parvovirus / protoparvovirus
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 speciesBufavirus-1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsMietzsch, M. / Agbandje-McKenna, M.
CitationJournal: Viruses / Year: 2018
Title: Atomic Resolution Structures of Human Bufaviruses Determined by Cryo-Electron Microscopy.
Authors: Maria Ilyas / Mario Mietzsch / Shweta Kailasan / Elina Väisänen / Mengxiao Luo / Paul Chipman / J Kennon Smith / Justin Kurian / Duncan Sousa / Robert McKenna / Maria Söderlund-Venermo / ...Authors: Maria Ilyas / Mario Mietzsch / Shweta Kailasan / Elina Väisänen / Mengxiao Luo / Paul Chipman / J Kennon Smith / Justin Kurian / Duncan Sousa / Robert McKenna / Maria Söderlund-Venermo / Mavis Agbandje-McKenna /
Abstract: Bufavirus strain 1 (BuV1), a member of the genus of the , was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated ...Bufavirus strain 1 (BuV1), a member of the genus of the , was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 Å, respectively. The BuVs, 65-73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core β-barrel (βB-βI), α-helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _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
1: VP2
2: VP2
3: VP2
4: VP2
5: VP2
6: 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
7: VP2
0: VP2


Theoretical massNumber of molelcules
Total (without water)3,694,07760
Polymers3,694,07760
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area944680 Å2
ΔGint-4235 kcal/mol
Surface area893410 Å2

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Components

#1: Protein ...
VP2


Mass: 61567.953 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bufavirus-1 / Gene: BF-003 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A097PIK3

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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)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellName: BuV1 capsid
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 / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1961
Image scansMovie frames/image: 60 / Used frames/image: 3-30

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Processing

SoftwareName: PHENIX / Version: 1.10-2155_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1Auto3DEM4.05.2particle selectionautopp M used for autoboxing
4Auto3DEM4.05.2CTF correction
7UCSF Chimeramodel fitting
9Auto3DEM4.05.2initial Euler assignment
12Auto3DEM4.05.23D reconstruction
13Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 59170
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29596 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01270060
ELECTRON MICROSCOPYf_angle_d0.94369480
ELECTRON MICROSCOPYf_dihedral_angle_d12.455214080
ELECTRON MICROSCOPYf_chiral_restr0.05837740
ELECTRON MICROSCOPYf_plane_restr0.00748780

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