+Open data
-Basic information
Entry | Database: PDB / ID: 8tey | |||||||||
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Title | Avian Adeno-associated virus - empty capsid | |||||||||
Components | Capsid protein | |||||||||
Keywords | VIRUS / Adeno-associated virus / capsid / quail bronchitis / avianAAV / AAAV | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Avian adeno-associated virus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
Authors | Hsi, J. / Mietzsch, M. / Chipman, P. / Afione, S. / Zeher, A. / Huang, R. / Chiorini, J. / McKenna, R. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J Virol / Year: 2023 Title: Structural and antigenic characterization of the avian adeno-associated virus capsid. Authors: Jane Hsi / Mario Mietzsch / Paul Chipman / Sandra Afione / Allison Zeher / Rick Huang / John Chiorini / Robert McKenna / Abstract: AAVs are extensively studied as promising therapeutic gene delivery vectors. In order to circumvent pre-existing antibodies targeting primate-based AAV capsids, the AAAV capsid was evaluated as an ...AAVs are extensively studied as promising therapeutic gene delivery vectors. In order to circumvent pre-existing antibodies targeting primate-based AAV capsids, the AAAV capsid was evaluated as an alternative to primate-based therapeutic vectors. Despite the high sequence diversity, the AAAV capsid was found to bind to a common glycan receptor, terminal galactose, which is also utilized by other AAVs already being utilized in gene therapy trials. However, contrary to the initial hypothesis, AAAV was recognized by approximately 30% of human sera tested. Structural and sequence comparisons point to conserved epitopes in the fivefold region of the capsid as the reason determinant for the observed cross-reactivity. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tey.cif.gz | 5.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8tey.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8tey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tey_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 8tey_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 8tey_validation.xml.gz | 650.7 KB | Display | |
Data in CIF | 8tey_validation.cif.gz | 1023.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/8tey ftp://data.pdbj.org/pub/pdb/validation_reports/te/8tey | HTTPS FTP |
-Related structure data
Related structure data | 41209MC 8texC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 60237.500 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Avian adeno-associated virus / Gene: Cap / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q7TG43 #2: Chemical | ChemComp-D5M / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Avian adeno-associated virus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Avian adeno-associated virus |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 61 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11240 / Symmetry type: POINT | ||||||||||||||||||||||||
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