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- PDB-9nzz: Adeno-associated virus 9 variant AAV9.AAA.VQVGRTS -

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Basic information

Entry
Database: PDB / ID: 9nzz
TitleAdeno-associated virus 9 variant AAV9.AAA.VQVGRTS
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: 1.84 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 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 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)59,0741
Polymers59,0741
Non-polymers00
Water10,521584
1
A: Capsid protein VP1
x 60


Theoretical massNumber of molelcules
Total (without water)3,544,45060
Polymers3,544,45060
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein Capsid protein VP1


Mass: 59074.168 Da / Num. of mol.: 1 / Mutation: N496A N497A N498A 455VQVGRTS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 9 / Strain: AAA.NVG7 / Gene: cap / Variant: AAA.NVG7 / Plasmid: pRGX.CMV / Production host: Homo sapiens (human) / References: UniProt: Q6JC40
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O
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
Details: NNN495-497AAA triple point mutation and insertion after S454 of VQVGRTS
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 5 MDa / Experimental value: NO
Source (natural)Organism: Adeno-associated virus 9 / Strain: AAA.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 phosphateKH2PO41
38 g/Lsodium chlorideNaCl1
41.15 g/Ldisodium phosphateNa2HPO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Concentration ~10^14 gc/mL
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
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: 1500 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 1700 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 recordingAverage exposure time: 2 sec. / Electron dose: 28.36 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2685
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2SerialEM3image acquisition
4cryoSPARC4CTF correction
10cryoSPARC4final Euler assignment
12cryoSPARC43D reconstruction
13PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 67287
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 1.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66738 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingPDB-ID: 7MTZ

7mtz


Pdb chain-ID: A / Accession code: 7MTZ / Source name: PDB / Type: experimental model

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