+Open data
-Basic information
Entry | Database: PDB / ID: 6ihb | ||||||
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Title | Adeno-Associated Virus 2 in complex with AAVR | ||||||
Components |
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Keywords | VIRUS / AAV2 | ||||||
Function / homology | Function and homology information permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell nucleolus / T=1 icosahedral viral capsid / neuron migration / cytoplasmic vesicle / clathrin-dependent endocytosis of virus by host cell / Golgi membrane / virion attachment to host cell / nucleolus ...permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell nucleolus / T=1 icosahedral viral capsid / neuron migration / cytoplasmic vesicle / clathrin-dependent endocytosis of virus by host cell / Golgi membrane / virion attachment to host cell / nucleolus / structural molecule activity / Golgi apparatus / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Adeno-associated virus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 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 | 6ihb.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ihb.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ihb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ihb_validation.pdf.gz | 904.7 KB | Display | wwPDB validaton report |
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Full document | 6ihb_full_validation.pdf.gz | 910.9 KB | Display | |
Data in XML | 6ihb_validation.xml.gz | 24 KB | Display | |
Data in CIF | 6ihb_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/6ihb ftp://data.pdbj.org/pub/pdb/validation_reports/ih/6ihb | HTTPS FTP |
-Related structure data
Related structure data | 9672MC 9671C 6ih9C 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: 10314.450 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0319L, AAVR, KIAA1837, PP791 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IZA0 |
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#2: Protein | Mass: 82031.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Adeno-associated virus 2 (isolate Srivastava/1982) References: UniProt: P03135 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | Electron dose: 1.53 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16820 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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