+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9671 | |||||||||
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Title | Adeno-Associated Virus 2 at 2.8 ang | |||||||||
Map data | ||||||||||
Sample |
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Keywords | AAV2 / VIRUS | |||||||||
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 / 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 (isolate Srivastava/1982) / Ao-associated virus 2 (isolate Srivastava/1982) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Lou ZY / Zhang R | |||||||||
Funding support | China, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9671.map.gz | 49.8 MB | EMDB map data format | |
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Header (meta data) | emd-9671-v30.xml emd-9671.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | emd_9671.png | 134.8 KB | ||
Filedesc metadata | emd-9671.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9671 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9671 | HTTPS FTP |
-Related structure data
Related structure data | 6ih9MC 9672C 6ihbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9671.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Ao-associated virus 2 (isolate Srivastava/1982)
Entire | Name: Ao-associated virus 2 (isolate Srivastava/1982) |
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Components |
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-Supramolecule #1: Ao-associated virus 2 (isolate Srivastava/1982)
Supramolecule | Name: Ao-associated virus 2 (isolate Srivastava/1982) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 648242 Sci species name: Ao-associated virus 2 (isolate Srivastava/1982) Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Virus shell | Shell ID: 1 / Diameter: 280.0 Å |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Adeno-associated virus 2 (isolate Srivastava/1982) Strain: isolate Srivastava/1982 |
Molecular weight | Theoretical: 58.644492 KDa |
Sequence | String: DGVGNSSGNW HCDSTWMGDR VITTSTRTWA LPTYNNHLYK QISSQSGASN DNHYFGYSTP WGYFDFNRFH CHFSPRDWQR LINNNWGFR PKRLNFKLFN IQVKEVTQND GTTTIANNLT STVQVFTDSE YQLPYVLGSA HQGCLPPFPA DVFMVPQYGY L TLNNGSQA ...String: DGVGNSSGNW HCDSTWMGDR VITTSTRTWA LPTYNNHLYK QISSQSGASN DNHYFGYSTP WGYFDFNRFH CHFSPRDWQR LINNNWGFR PKRLNFKLFN IQVKEVTQND GTTTIANNLT STVQVFTDSE YQLPYVLGSA HQGCLPPFPA DVFMVPQYGY L TLNNGSQA VGRSSFYCLE YFPSQMLRTG NNFTFSYTFE DVPFHSSYAH SQSLDRLMNP LIDQYLYYLS RTNTPSGTTT QS RLQFSQA GASDIRDQSR NWLPGPCYRQ QRVSKTSADN NNSEYSWTGA TKYHLNGRDS LVNPGPAMAS HKDDEEKFFP QSG VLIFGK QGSEKTNVDI EKVMITDEEE IRTTNPVATE QYGSVSTNLQ RGNRQAATAD VNTQGVLPGM VWQDRDVYLQ GPIW AKIPH TDGHFHPSPL MGGFGLKHPP PQILIKNTPV PANPSTTFSA AKFASFITQY STGQVSVEIE WELQKENSKR WNPEI QYTS NYNKSVNVDF TVDTNGVYSE PRPIGTRYLT RNL UniProtKB: Capsid protein VP1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I |
Details | The AAV2 particles are purified fron 293T cell, with the yeild of approximately 10^12vg per 10L. |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Frames/image: 1-19 / Number grids imaged: 1 / Average exposure time: 1.2 sec. / Average electron dose: 1.53 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) Software - details: RELION2.1 was used for the final reconstruction software. Number images used: 14434 |