+Open data
-Basic information
Entry | Database: PDB / ID: 8fq4 | ||||||
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Title | AAV1 VP3 Only Capsid | ||||||
Components | Capsid protein | ||||||
Keywords | VIRUS LIKE PARTICLE / AAV / gene therapy / capsid / VP3 | ||||||
Function / homology | Phospholipase 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 species | Adeno-associated virus - 1 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.27 Å | ||||||
Authors | Mietzsch, M. / McKenna, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol Ther Methods Clin Dev / Year: 2023 Title: Production and characterization of an AAV1-VP3-only capsid: An analytical benchmark standard. Authors: Mario Mietzsch / Weijing Liu / Ke Ma / Antonette Bennett / Austin R Nelson / Keely Gliwa / Paul Chipman / Xiaofeng Fu / Shane Bechler / Robert McKenna / Rosa Viner / Abstract: Adeno-associated viruses (AAVs) are non-enveloped ssDNA icosahedral T = 1 viruses used as vectors for clinical gene delivery. Currently, there are over 200 AAV-related clinical trials and six ...Adeno-associated viruses (AAVs) are non-enveloped ssDNA icosahedral T = 1 viruses used as vectors for clinical gene delivery. Currently, there are over 200 AAV-related clinical trials and six approved biologics on the market. As such new analytical methods are continually being developed to characterize and monitor the quality and purity of manufactured AAV vectors, these include ion-exchange chromatography and Direct Mass Technology. However, these methods require homogeneous analytical standards with a high molecular weight standard comparable to the mass of an AAV capsid. Described here is the design, production, purification, characterization, and the cryo-electron microscopy structure of an AAV1-VP3-only capsid that fulfills this need as a calibrant to determine capsid mass, charge, homogeneity, and transgene packaging characteristics. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fq4.cif.gz | 5.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8fq4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fq4_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8fq4_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8fq4_validation.xml.gz | 613.3 KB | Display | |
Data in CIF | 8fq4_validation.cif.gz | 1 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/8fq4 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/8fq4 | HTTPS FTP |
-Related structure data
Related structure data | 29377MC 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: 58299.422 Da / Num. of mol.: 60 / Fragment: UNP residues 218-736 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Adeno-associated virus - 1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9WBP8 |
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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: Adeno-associated virus - 1 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 3.57 MDa / Experimental value: YES |
Source (natural) | Organism: Adeno-associated virus - 1 |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK 293 |
Details of virus | Empty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE |
Virus shell | Triangulation number (T number): 1 |
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: 1840 nm / Nominal defocus min: 480 nm / Cs: 2.7 mm |
Image recording | Electron dose: 59 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.10-2155_2155: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4418 / Symmetry type: POINT | ||||||||||||||||||||||||
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