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- PDB-6x2k: The Tusavirus (TuV) capsid structure -

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Basic information

Entry
Database: PDB / ID: 6x2k
TitleThe Tusavirus (TuV) capsid structure
ComponentsVP2
KeywordsVIRUS / Icosahedral Capsid / Tusavirus / TuV / Protoparvovirus
Function / homologyParvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Parvovirus coat protein VP1/VP2 / viral capsid / structural molecule activity / VP2
Function and homology information
Biological speciesTusavirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsMietzsch, 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: Viruses / Year: 2020
Title: Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology.
Authors: Mario Mietzsch / Robert McKenna / Elina Väisänen / Jennifer C Yu / Maria Ilyas / Joshua A Hull / Justin Kurian / J Kennon Smith / Paul Chipman / Yi Lasanajak / David Smith / Maria ...Authors: Mario Mietzsch / Robert McKenna / Elina Väisänen / Jennifer C Yu / Maria Ilyas / Joshua A Hull / Justin Kurian / J Kennon Smith / Paul Chipman / Yi Lasanajak / David Smith / Maria Söderlund-Venermo / Mavis Agbandje-McKenna /
Abstract: Several members of the genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used ...Several members of the genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used cryo-electron microscopy and image reconstruction to determine their capsid structures to ~2.9 Å resolution, and glycan array and cell-based assays to identify glycans utilized for cellular entry. Structural comparisons show that the CuV and TuV capsids share common features with other parvoviruses, including an eight-stranded anti-parallel β-barrel, depressions at the icosahedral 2-fold and surrounding the 5-fold axes, and a channel at the 5-fold axes. However, the viruses exhibit significant topological differences in their viral protein surface loops. These result in three separated 3-fold protrusions, similar to the bufaviruses also infecting humans, suggesting a host-driven structure evolution. The surface loops contain residues involved in receptor binding, cellular trafficking, and antigenic reactivity in other parvoviruses. In addition, terminal sialic acid was identified as the glycan potentially utilized by both CuV and TuV for cellular entry, with TuV showing additional recognition of poly-sialic acid and sialylated Lewis X (sLeXLeXLeX) motifs reported to be upregulated in neurotropic and cancer cells, respectively. These structures provide a platform for annotating the cellular interactions of these human pathogens.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release

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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)3,672,28960
Polymers3,672,28960
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: 61204.824 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tusavirus 1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A097F8N9

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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: Tusavirus 1 / Type: VIRUS / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Tusavirus 1
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
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
Image recordingElectron dose: 75 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: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33191 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011267000
ELECTRON MICROSCOPYf_angle_d1.011366240
ELECTRON MICROSCOPYf_dihedral_angle_d11.571210840
ELECTRON MICROSCOPYf_chiral_restr0.05940080
ELECTRON MICROSCOPYf_plane_restr0.00748180

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