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- PDB-7jot: Adeno-associated virus strain AAV7 capsid icosahedral structure -

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Basic information

Entry
Database: PDB / ID: 7jot
TitleAdeno-associated virus strain AAV7 capsid icosahedral structure
ComponentsCapsid protein
KeywordsVIRUS / AAV / parvovirus / Parvoviridae / adeno-associated virus / capsid
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
Function and homology information
Biological speciesAdeno-associated virus - 7
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFirlar, E. / Yost, S.A. / Mercer, A.C. / Kaelber, J.T.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2020
Title: Structure of the AAVhu.37 capsid by cryoelectron microscopy.
Authors: Jason T Kaelber / Samantha A Yost / Keith A Webber / Emre Firlar / Ye Liu / Olivier Danos / Andrew C Mercer /
Abstract: Adeno-associated viruses (AAVs) are used as in vivo gene-delivery vectors in gene-therapy products and have been heavily investigated for numerous indications. Over 100 naturally occurring AAV ...Adeno-associated viruses (AAVs) are used as in vivo gene-delivery vectors in gene-therapy products and have been heavily investigated for numerous indications. Over 100 naturally occurring AAV serotypes and variants have been isolated from primate samples. Many reports have described unique properties of these variants (for instance, differences in potency, target cell or evasion of the immune response), despite high amino-acid sequence conservation. AAVhu.37 is of interest for clinical applications owing to its proficient transduction of the liver and central nervous system. The sequence identity of the AAVhu.37 VP1 to the well characterized AAVrh.10 serotype, for which no structure is available, is greater than 98%. Here, the structure of the AAVhu.37 capsid at 2.56 Å resolution obtained via single-particle cryo-electron microscopy is presented.
History
DepositionAug 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-22412
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  • Superimposition on EM map
  • EMDB-22412
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)58,4391
Polymers58,4391
Non-polymers00
Water00
1
A: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,506,31360
Polymers3,506,31360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
x 5


  • icosahedral pentamer
  • 292 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)292,1935
Polymers292,1935
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 351 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)350,6316
Polymers350,6316
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein / VP3


Mass: 58438.547 Da / Num. of mol.: 1 / Fragment: UNP residues 220-737
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 7 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8JQG0

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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 - 7 / Type: VIRUS
Details: Virions containing GFP-encoding ssDNA were assembled in transfected HEK293T helper cells.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 5 MDa / Experimental value: NO
Source (natural)Organism: Adeno-associated virus - 7
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 250 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4 / Details: PBS
Buffer component
IDConc.NameFormulaBuffer-ID
19.0 g/Lsodium chlorideNaCl1
20.144 g/Lpotassium phosphate dibasicKH2PO41
30.795 g/Lsodium phosphate monobasicNa2HPO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: approx. 8*10^14 genome copies per mL
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K / Details: Whatman #1 filter paper

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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 / Calibrated defocus min: 244 nm / Calibrated defocus max: 2836 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 1.064 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2430
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 30 / Used frames/image: 1-30

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2SerialEM3.7image acquisition
4RELION3.1-betaCTF correction
7Coot0.8.9.2model fitting
9PHENIXdev-3366model refinement
10RELION3.1-betainitial Euler assignment
11RELION3.1-betafinal Euler assignment
12RELION3.1-betaclassification
13RELION3.1-beta3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 103227
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71811 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 6U95

6u95


Pdb chain-ID: A / Accession code: 6U95 / Source name: PDB / Type: experimental model

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