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 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.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 digital issues and online access to articles
$119.00 per year
only $9.92 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Data availability
The obtained cryo-EM density maps and the data of the resolved structures were deposited into the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB) with the following accession numbers: AAV2, EMD-9671 and 6IH9; AAV2–AAVR complex, EMD-9672 and 6IHB. All other data supporting the findings of this study are available from the corresponding authors upon request.
References
Zinn, E. & Vandenberghe, L. H. Adeno-associated virus: fit to serve. Curr. Opin. Virol. 8, 90–97 (2014).
Lisowski, L. et al. Selection and evaluation of clinically relevant AAV variants in a xenograft liver model. Nature 506, 382–386 (2014).
Kotterman, M. A. & Schaffer, D. V. Engineering adeno-associated viruses for clinical gene therapy. Nat. Rev. Genet. 15, 445–451 (2014).
Deverman, B. E., Ravina, B. M., Bankiewicz, K. S., Paul, S. M. & Sah, D. W. Y. Gene therapy for neurological disorders: progress and prospects. Nat. Rev. Drug Discov. 17, 641–659 (2018); erratum 17, 767 (2018).
Nathwani, A. C. et al. Adenovirus-associated virus vector-mediated gene transfer in hemophilia B. N. Engl. J. Med. 365, 2357–2365 (2011).
Miller, N. Glybera and the future of gene therapy in the European Union. Nat. Rev. Drug. Discov. 11, 419 (2012).
Dias, M. F. et al. Molecular genetics and emerging therapies for retinitis pigmentosa: basic research and clinical perspectives. Prog. Retin. Eye Res. 63, 107–131 (2018).
Linden, R. M. & Berns, K. I. Molecular biology of adeno-associated viruses. Contrib. Microbiol. 4, 68–84 (2000).
Agbandje-McKenna, M. & Kleinschmidt, J. AAV capsid structure and cell interactions. Methods Mol. Biol. 807, 47–92 (2011).
Burg, M. et al. Atomic structure of a rationally engineered gene delivery vector, AAV2.5. J. Struct. Biol. 203, 236–241 (2018).
Govindasamy, L. et al. Structural insights into adeno-associated virus serotype 5. J. Virol. 87, 11187–11199 (2013).
Halder, S. et al. Structure of neurotropic adeno-associated virus AAVrh.8. J. Struct. Biol. 192, 21–36 (2015).
Lerch, T. F. & Chapman, M. S. Identification of the heparin binding site on adeno-associated virus serotype 3B (AAV-3B). Virology 423, 6–13 (2012).
Padron, E. et al. Structure of adeno-associated virus type 4. J. Virol. 79, 5047–5058 (2005).
Xie, Q. et al. The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy. Proc. Natl Acad. Sci. USA 99, 10405–10410 (2002).
Xie, Q. et al. The 2.8 Å electron microscopy structure of adeno-associated virus-DJ bound by a heparinoid pentasaccharide. Mol. Ther. Methods Clin. Dev. 5, 1–12 (2017).
McCraw, D. M., O'Donnell, J. K., Taylor, K. A., Stagg, S. M. & Chapman, M. S. Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20. Virology 431, 40–49 (2012).
Summerford, C. & Samulski, R. J. Membrane-associated heparan sulfate proteoglycan is a receptor for adeno-associated virus type 2 virions. J. Virol. 72, 1438–1445 (1998).
Kashiwakura, Y. et al. Hepatocyte growth factor receptor is a coreceptor for adeno-associated virus type 2 infection. J. Virol. 79, 609–614 (2005).
Qing, K. et al. Human fibroblast growth factor receptor 1 is a co-receptor for infection by adeno-associated virus 2. Nat. Med. 5, 71–77 (1999).
Pillay, S. et al. An essential receptor for adeno-associated virus infection. Nature 530, 108–112 (2016).
Ibraghimov-Beskrovnaya, O. et al. Strong homophilic interactions of the Ig-like domains of polycystin-1, the protein product of an autosomal dominant polycystic kidney disease gene, PKD1. Hum. Mol. Genet. 9, 1641–1649 (2000).
Pillay, S. et al. AAV serotypes have distinctive interactions with domains of the cellular receptor AAVR. J. Virol. https://doi.org/10.1128/JVI.00391-17 (2017).
Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
Hu, M. et al. A particle-filter framework for robust cryo-EM 3D reconstruction. Nat. Methods 15, 1083–1089 (2018).
Pillay, S. & Carette, J. E. Host determinants of adeno-associated viral vector entry. Curr. Opin. Virol. 24, 124–131 (2017).
Couto, J. M. et al. The KIAA0319-like (KIAA0319L) gene on chromosome 1p34 as a candidate for reading disabilities. J. Neurogenet. 22, 295–313 (2008).
Platt, M. P. et al. Embryonic disruption of the candidate dyslexia susceptibility gene homolog Kiaa0319-like results in neuronal migration disorders. Neuroscience 248, 585–593 (2013).
Li, X. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10, 584–590 (2013).
Mindell, J. A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Afonine, P. V. et al. New tools for the analysis and validation of cryo-EM maps and atomic models. bioRxiv https://doi.org/10.1101/279844 (2018).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
Acknowledgements
The authors thank the Computing and Cryo-EM Platforms of Tsinghua University, Branch of the National Center for Protein Sciences (Beijing) for providing facilities. They also thank L. Chen for his help in data collection, D. Yan for his assistance in molecular cloning, W. Huang for her help in cell culture, and Q. Ding for his discussion and comments. This work was supported by the National Program on Key Research Project of China (2017YFC0840300 and 2018YFA0507200) and the National Natural Science Foundation of China (grant numbers 81322023, 31770309, 81372284, 81520108019 and 31370733).
Author information
Authors and Affiliations
Contributions
Z.L., W.D. and Z.R. conceived the project. Z.L. and W.D. designed the experiments. Ra.Z., L.C., M.C., Z.S., M.H., Ro.Z., W.S., X.Z. and Z.Y. performed virus and protein purification, cryo-EM data collection and processing. Ra.Z., L.C., X.L., Y.S., S.L., W.D. and Z.L. analysed the data. Z.L., W.D. and Z.R. wrote the manuscript. All authors discussed the experiments, read and approved the manuscript.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Supplementary Information
Supplementary Figures 1–12 and Supplementary Tables 1–6.
Rights and permissions
About this article
Cite this article
Zhang, R., Cao, L., Cui, M. et al. Adeno-associated virus 2 bound to its cellular receptor AAVR. Nat Microbiol 4, 675–682 (2019). https://doi.org/10.1038/s41564-018-0356-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41564-018-0356-7
This article is cited by
-
Biophysical characterization of adeno-associated virus capsid through the viral transduction life cycle
Journal of Genetic Engineering and Biotechnology (2023)
-
A custom-made AAV1 variant (AAV1-T593K) enables efficient transduction of Japanese quail neurons in vitro and in vivo
Communications Biology (2023)
-
Hardwiring tissue-specific AAV transduction in mice through engineered receptor expression
Nature Methods (2023)
-
Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates
Nature Communications (2023)
-
AAV capsid variants with brain-wide transgene expression and decreased liver targeting after intravenous delivery in mouse and marmoset
Nature Neuroscience (2022)