+Open data
-Basic information
Entry | Database: PDB / ID: 6ih9 | ||||||
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Title | Adeno-Associated Virus 2 at 2.8 ang | ||||||
Components | Capsid protein VP1 | ||||||
Keywords | VIRUS / AAV2 | ||||||
Function / homology | Function and homology information symbiont entry into host cell via permeabilization of host membrane / host cell nucleolus / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity Similarity search - Function | ||||||
Biological species | Adeno-associated virus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Lou, Z.Y. / Zhang, R. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Microbiol / Year: 2019 Title: Adeno-associated virus 2 bound to its cellular receptor AAVR. Authors: Ran Zhang / Lin Cao / Mengtian Cui / Zixian Sun / Mingxu Hu / Rouxuan Zhang / William Stuart / Xiaochu Zhao / Zirui Yang / Xueming Li / Yuna Sun / Shentao Li / Wei Ding / Zhiyong Lou / Zihe Rao / Abstract: Adeno-associated virus (AAV) is a leading vector for virus-based gene therapy. The receptor for AAV (AAVR; also named KIAA0319L) was recently identified, and the precise characterization of AAV-AAVR ...Adeno-associated virus (AAV) is a leading vector for virus-based gene therapy. The receptor for AAV (AAVR; also named KIAA0319L) was recently identified, and the precise characterization of AAV-AAVR recognition is in immediate demand. Taking advantage of a particle-filtering algorithm, we report here the cryo-electron microscopy structure of the AAV2-AAVR complex at 2.8 Å resolution. This structure reveals that of the five Ig-like polycystic kidney disease (PKD) domains in AAVR, PKD2 binds directly to the spike region of the AAV2 capsid adjacent to the icosahedral three-fold axis. Residues in strands B and E, and the BC loop of AAVR PKD2 interact directly with the AAV2 capsid. The interacting residues in the AAV2 capsid are mainly in AAV-featured variable regions. Mutagenesis of the amino acids at the AAV2-AAVR interface reduces binding activity and viral infectivity. Our findings provide insights into the biology of AAV entry with high-resolution details, providing opportunities for the development of new AAV vectors for gene therapy. | ||||||
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 | 6ih9.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ih9.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ih9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ih9_validation.pdf.gz | 866.6 KB | Display | wwPDB validaton report |
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Full document | 6ih9_full_validation.pdf.gz | 868.4 KB | Display | |
Data in XML | 6ih9_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 6ih9_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/6ih9 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/6ih9 | HTTPS FTP |
-Related structure data
Related structure data | 9671MC 9672C 6ihbC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 58644.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Adeno-associated virus 2 (isolate Srivastava/1982) Strain: isolate Srivastava/1982 / References: UniProt: P03135 |
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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: Ao-associated virus 2 (isolate Srivastava/1982) / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Ao-associated virus 2 (isolate Srivastava/1982) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Virus shell | Diameter: 280 nm |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The AAV2 particles are purified fron 293T cell, with the yeild of approximately 10^12vg per 10L. |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Average exposure time: 1.2 sec. / Electron dose: 1.53 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 |
Image scans | Movie frames/image: 19 / Used frames/image: 1-19 |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14434 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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