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- PDB-9n5x: The capsid structure of AAVpo.1 -

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Basic information

Entry
Database: PDB / ID: 9n5x
TitleThe capsid structure of AAVpo.1
ComponentsVP3
KeywordsVIRUS / AAVpo.1 / porcine adeno-associated virus / gene therapy / vector / 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 / VP3
Function and homology information
Biological speciesAdeno-associated virus - Po1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.79 Å
AuthorsNelson, A. / 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: To Be Published
Title: Structural insights into porcine adeno-associated viruses
Authors: Nelson, A. / Mietzsch, M. / Eby, J. / Chipman, P. / McKenna, R.
History
DepositionFeb 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 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: VP3
B: VP3
C: VP3
D: VP3
E: VP3
F: VP3
G: VP3
H: VP3
I: VP3
J: VP3
K: VP3
L: VP3
M: VP3
N: VP3
O: VP3
P: VP3
Q: VP3
R: VP3
S: VP3
T: VP3
U: VP3
V: VP3
W: VP3
X: VP3
Y: VP3
Z: VP3
a: VP3
b: VP3
c: VP3
d: VP3
e: VP3
f: VP3
g: VP3
h: VP3
i: VP3
j: VP3
k: VP3
l: VP3
m: VP3
n: VP3
o: VP3
p: VP3
q: VP3
r: VP3
s: VP3
t: VP3
u: VP3
v: VP3
w: VP3
x: VP3
y: VP3
z: VP3
1: VP3
2: VP3
3: VP3
4: VP3
5: VP3
6: VP3
7: VP3
8: VP3


Theoretical massNumber of molelcules
Total (without water)3,611,10760
Polymers3,611,10760
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 ...
VP3


Mass: 60185.117 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - Po1 / Strain: AAVpo.1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: C0LA99
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: Adeno-associated virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Adeno-associated virus / Strain: AAVpo.1
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
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: 2200 nm / Nominal defocus min: 800 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: NONE
3D reconstructionResolution: 1.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 512823 / 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_d0.91352140
ELECTRON MICROSCOPYf_dihedral_angle_d8.303203640
ELECTRON MICROSCOPYf_chiral_restr0.06636540
ELECTRON MICROSCOPYf_plane_restr0.00746800

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