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- PDB-9me0: Goose Parvovirus Capsid -

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Basic information

Entry
Database: PDB / ID: 9me0
TitleGoose Parvovirus Capsid
ComponentsVP1
KeywordsVIRUS LIKE PARTICLE / GPV / capsid / cryo-EM / parvovirus / gene therapy / vector
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 speciesGoose parvovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsJabbari, K. / Mietzsch, M. / McKenna, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: Microorganisms / Year: 2025
Title: The Structural, Biophysical, and Antigenic Characterization of the Goose Parvovirus Capsid.
Authors: Korosh Jabbari / Mario Mietzsch / Jane Hsi / Paul Chipman / Jianming Qiu / Robert McKenna /
Abstract: Goose parvovirus (GPV) is an etiological agent of Derzsy's disease, afflicting geese and Muscovy ducks worldwide. Its high mortality rate among goslings and ducklings causes large losses to the ...Goose parvovirus (GPV) is an etiological agent of Derzsy's disease, afflicting geese and Muscovy ducks worldwide. Its high mortality rate among goslings and ducklings causes large losses to the waterfowl industry. Toward molecular and structural characterization, virus-like particles (VLPs) of GPV were produced, and the capsid structure was determined by cryogenic electron microscopy (cryo-EM) at a resolution of 2.4 Å. The capsid exhibited structural features conserved among parvoviruses, including surface two-fold depressions, three-fold protrusions, and five-fold channels. A structural comparison of the GPV viral protein (VP) structure with other adeno-associated viruses (AAVs), including human AAV2, AAV5, and quail AAV (QAAV), revealed unique conformations of several surface-accessible variable regions (VRs). Furthermore, the GPV capsid was found to be thermally stable at physiological pH, but less so under lower pH conditions. As a member of the genus , GPV could also be bound by cross-reactive anti-AAV capsid antibodies that bind to the five-fold region of the viruses, as shown by native immuno-dot blot analysis. Finally, the GPV VP structure was compared to those of other bird dependoparvoviruses, which revealed that VR-III may be important for GPV and Muscovy duck parvovirus (MDPV) infection.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: 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


Theoretical massNumber of molelcules
Total (without water)4,893,06360
Polymers4,893,06360
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
VP1


Mass: 81551.055 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Goose parvovirus / Gene: vp1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q67666
Has protein modificationN

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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: Goose parvovirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Goose parvovirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: SF9
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4700 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.10-2155_2155 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15471 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01257640
ELECTRON MICROSCOPYf_angle_d0.86351660
ELECTRON MICROSCOPYf_dihedral_angle_d8.38204480
ELECTRON MICROSCOPYf_chiral_restr0.05936420
ELECTRON MICROSCOPYf_plane_restr0.00646440

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