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Yorodumi- PDB-7kp3: Adeno-associated virus serotype 5 at 2.1 Angstroms resolution, AAV5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kp3 | ||||||
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Title | Adeno-associated virus serotype 5 at 2.1 Angstroms resolution, AAV5 | ||||||
Components | Capsid proteinCapsid | ||||||
Keywords | VIRUS / AAV5 / AAV / AAV-5 / Adeno Associated Virus / VIRUS LIKE PARTICLE / parvovirus / gene therapy | ||||||
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 - 5 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å | ||||||
Authors | Silveria, M. / Chapman, M.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Viruses / Year: 2020 Title: The Structure of an AAV5-AAVR Complex at 2.5 Å Resolution: Implications for Cellular Entry and Immune Neutralization of AAV Gene Therapy Vectors. Authors: Mark A Silveria / Edward E Large / Grant M Zane / Tommi A White / Michael S Chapman / Abstract: Adeno-Associated Virus is the leading vector for gene therapy. Although it is the vector for all in vivo gene therapies approved for clinical use by the US Food and Drug Administration, its biology ...Adeno-Associated Virus is the leading vector for gene therapy. Although it is the vector for all in vivo gene therapies approved for clinical use by the US Food and Drug Administration, its biology is still not yet fully understood. It has been shown that different serotypes of AAV bind to their cellular receptor, AAVR, in different ways. Previously we have reported a 2.4Å structure of AAV2 bound to AAVR that shows ordered structure for only one of the two AAVR domains with which AAV2 interacts. In this study we present a 2.5Å resolution structure of AAV5 bound to AAVR. AAV5 binds to the first polycystic kidney disease (PKD) domain of AAVR that was not ordered in the AAV2 structure. Interactions of AAV5 with AAVR are analyzed in detail, and the implications for AAV2 binding are explored through molecular modeling. Moreover, we find that binding sites for the antibodies ADK5a, ADK5b, and 3C5 on AAV5 overlap with the binding site of AAVR. These insights provide a structural foundation for development of gene therapy agents to better evade immune neutralization without disrupting cellular entry. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7kp3.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kp3.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 7kp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/7kp3 ftp://data.pdbj.org/pub/pdb/validation_reports/kp/7kp3 | HTTPS FTP |
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-Related structure data
Related structure data | 22987MC 7kpnC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 80366.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Adeno-associated virus - 5 / Gene: cap, VP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9YIJ1 |
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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 / Type: VIRUS Details: Expressed using SF9 cells with a pfastbac LIC vector. Purified with cesium chloride ultracentrifugation. Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 3.746 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Adeno-associated virus | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||||||||||
Virus shell | Diameter: 250 nm / Triangulation number (T number): 1 | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K Details: Two 2uL aliquots applied to grid (manual blotting between), prior to automated 3 second blot before plunging. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS Details: Coma-free alignment and objective astigmatism where corrected using Sherpa (Thermo Fisher, Inc.). |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: -2700 nm / Nominal defocus min: -700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93 K / Temperature (min): 93 K |
Image recording | Electron dose: 31.7 e/Å2 / Detector mode: INTEGRATING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9490 / Details: Pixel size was 0.5295 angstrom. |
Image scans | Width: 11520 / Height: 8184 |
-Processing
EM software |
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CTF correction | Details: CTF correction was performed on a per particle basis. Type: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 672106 Details: LoG Picker was used for initial automated particle selection. Templates were then generated by 2D classification, followed by particle template selection in Relion 3.1 beta. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 373426 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Least-squares residual Details: Stand-alone RSRef was used for refinement of magnification, resolution, envelope correction and atomic B-factors. This was alternated with RSRef-embedded CNS was used for molecular dynamics ...Details: Stand-alone RSRef was used for refinement of magnification, resolution, envelope correction and atomic B-factors. This was alternated with RSRef-embedded CNS was used for molecular dynamics optimization (1st round) and stereochemically-restrained all-atom least-squares optimization. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3NTT Accession code: 3NTT / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 2.1 Å |