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- PDB-9o0f: Adeno-associated virus 9 variant AAV9.NVG7 -

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Basic information

Entry
Database: PDB / ID: 9o0f
TitleAdeno-associated virus 9 variant AAV9.NVG7
ComponentsCapsid protein VP1
KeywordsVIRUS LIKE PARTICLE / parvovirus / virion / targeting / engineered
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 / Capsid protein VP1
Function and homology information
Biological speciesAdeno-associated virus 9
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsChoi, H. / Hou, C.F.D. / Firnberg, E. / Wei, H. / Petrou, V.I. / Kaelber, J.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Performance of low-voltage cryo-electron microscopes
Authors: Choi, H. / Hou, C.F.D. / Firnberg, E. / Wei, H. / Petrou, V.I. / Kaelber, J.T.
History
DepositionApr 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 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

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Assembly

Deposited unit
A: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)59,2031
Polymers59,2031
Non-polymers00
Water00
1
A: Capsid protein VP1
x 60


Theoretical massNumber of molelcules
Total (without water)3,552,19560
Polymers3,552,19560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein Capsid protein VP1


Mass: 59203.246 Da / Num. of mol.: 1 / Mutation: 455VQVGRTS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 9 / Strain: NVG7 / Gene: cap / Variant: NVG7 / Plasmid: pRGX.CMV / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6JC40
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 9 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 5 MDa / Experimental value: NO
Source (natural)Organism: Adeno-associated virus 9 / Strain: AAV9.NVG7
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 / Plasmid: pRGX.CMV
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 226 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4 / Details: PBS pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
10.2 g/Lpotassium chlorideKCl1
20.2 g/Lmonopotassium pohosphateKH2PO41
38 g/Lsodium chlorideNaCl1
41.15 g/Ldisodium phosphateNa2HPO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20.46 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3813
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 1-50

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2PHENIX1.21rc1_5015model refinement
5cryoSPARC4CTF correction
10cryoSPARC4initial Euler assignment
11cryoSPARC4final Euler assignment
12cryoSPARC4classification
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10924
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6436 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingPDB-ID: 9NZZ

9nzz


Pdb chain-ID: A / Accession code: 9NZZ / Source name: PDB / Type: experimental model

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