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- PDB-9n5l: The Red Crowned-Crane Parvovirus Capsid -

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Basic information

Entry
Database: PDB / ID: 9n5l
TitleThe Red Crowned-Crane Parvovirus Capsid
ComponentsMajor capsid protein
KeywordsVIRUS / RCPV / Aveparvovirus / Parvovirus / capsid / VLP / cryo-EM
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 / Major capsid protein
Function and homology information
Biological speciesRed-crowned crane parvovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsHsi, J. / Mietzsch, M. / McKenna, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-2236414 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: To Be Published
Title: Birds of a Feather Flock Together: Structural Characterization of Red-Crowned Crane and Turkey Aveparvoviruses
Authors: Hsi, J. / Mietzsch, M. / Patney, M. / Chen, S. / Sawh-Gopal, A. / Chipman, P. / McKenna, R.
History
DepositionFeb 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,537,285180
Polymers3,534,36960
Non-polymers2,917120
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 ...
Major capsid protein


Mass: 58906.148 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Red-crowned crane parvovirus / Gene: VP2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2K9YN80
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 120 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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: Red-crowned crane parvovirus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Red-crowned crane parvovirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 470 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.10-2155_2155 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 405850 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011246600
ELECTRON MICROSCOPYf_angle_d0.821336960
ELECTRON MICROSCOPYf_dihedral_angle_d8.205194100
ELECTRON MICROSCOPYf_chiral_restr0.05235220
ELECTRON MICROSCOPYf_plane_restr0.00544100

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