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Structural Insight into the Unique Properties of Adeno-Associated Virus Serotype 9
Open accessAbstract
Adeno-associated virus serotype 9 (AAV9) has enhanced capsid-associated tropism for cardiac muscle and the ability to cross the blood-brain barrier compared to other AAV serotypes. To help identify the structural features facilitating these properties, we have used cryo-electron microscopy (cryo-EM) and three-dimensional image reconstruction (cryo-reconstruction) and X-ray crystallography to determine the structure of the AAV9 capsid at 9.7- and 2.8-Å resolutions, respectively. The AAV9 capsid exhibits the surface topology conserved in all AAVs: depressions at each icosahedral two-fold symmetry axis and surrounding each five-fold axis, three separate protrusions surrounding each three-fold axis, and a channel at each five-fold axis. The AAV9 viral protein (VP) has a conserved core structure, consisting of an eight-stranded, β-barrel motif and the αA helix, which are present in all parvovirus structures. The AAV9 VP differs in nine variable surface regions (VR-I to -IX) compared to AAV4, but at only three (VR-I, VR-II, and VR-IV) compared to AAV2 and AAV8. VR-I differences modify the raised region of the capsid surface between the two-fold and five-fold depressions. The VR-IV difference produces smaller three-fold protrusions in AAV9 that are less “pointed” than AAV2 and AAV8. Significantly, residues in the AAV9 VRs have been identified as important determinants of cellular tropism and transduction and dictate its antigenic diversity from AAV2. Hence, the AAV9 VRs likely confer the unique infection phenotypes of this serotype.
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“Despite this conservation, no nucleotide was observed in the AAV2, AAV5, and AAV9 structures (DiMattia et al., 2012; Govindasamy et al., 2013; Guenther et al., 2019; Xie et al., 2002).”
From Structure comparison of the chimeric AAV2.7m8 vector with parental AAV2 (2020) · cites this paper as DiMattia et al., 2012
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Self-citationGene Therapy Approaches for Lysosomal Storage Disease: Next-Generation Treatment
Byrne, B. J., Falk, D. J., Clément, N., & Mah, C. S. (2012) · Human Gene Therapy · doi:10.1089/hum.2012.140 · Cited by 48
“More interestingly, rAAV9 has been shown to transduce neural tissue via retrograde transport after intramuscular delivery or even by crossing the blood–brain barrier itself (Foust et al., 2009; Bevan et al., 2011; Dayton et al., 2012; Dimattia et al., 2012; ElMallah et al., 2012).”
BackgroundSelf-citationCryo-electron Microscopy of Adeno-associated Virus
Stagg, S. M., Yoshioka, C., Davulcu, O., & Chapman, M. S. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00936 · Cited by 48
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Cabanes‐Creus, M., Westhaus, A., Navarro, R. G., Baltazar, G., Zhu, E., Amaya, A. K., Liao, S. H. Y., Scott, S., Sallard, E., Dilworth, K. L., et al. (2020) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2020.05.004 · Cited by 45
Self-citationPositron emission tomography imaging of novel AAV capsids maps rapid brain accumulation
Seo, J. W., Ingham, E. S., Mahakian, L. M., Tumbale, S. K., Wu, B., Aghevlian, S., Shams, S., Baikoghli, M., Jain, P., Ding, X., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15818-4 · Cited by 46
Dobrovolskaia, M. A., & Bathe, M. (2020) · Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology · doi:10.1002/wnan.1657 · Cited by 45
“(b ) Pseudoatomic model of AAV9 using AAV2 and AAV8 crystal structures as templates, showing the surface loops VR-I and VR-IV that control transduction phenotype and help determine tropism and antigenic reactivity in addition to transduction efficiency (DiMattia et al., 2012).”
Xu, G., Zhang, R., Li, H., Yin, K., Ma, X., & Lou, Z. (2022) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2022.05.009 · Cited by 43
The Liver as a Target Organ for Gene Therapy: State of the Art, Challenges, and Future Perspectives
Jacobs, F., Gordts, S. C., Muthuramu, I., & Geest, B. D. (2012) · Pharmaceuticals · doi:10.3390/ph5121372 · Cited by 40
Quantifying and comparing radiation damage in the Protein Data Bank
Shelley, K. L., & Garman, E. F. (2022) · Nature Communications · doi:10.1038/s41467-022-28934-0 · Cited by 45
The structure of AAVrh32.33, a novel gene delivery vector
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Self-citationAn adeno-associated virus variant enabling efficient ocular-directed gene delivery across species
Luo, S., Jiang, H., Li, Q., Qin, Y., Yang, S., Li, J., Xu, L., Gou, Y., Zhang, Y., Liu, F., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48221-4 · Cited by 39
“Toconstructthese capsid variants, we designed a set of 18 peptides, ranging from 5 to 14 amino acids in length, based on the known structural biology and cellular receptorology of AAV8 35 – 42 (Supplementary Table 1).”
Optimized Adeno-Associated Virus Vectors for Efficient Transduction of Human Retinal Organoids
Völkner, M., Pavlou, M., Büning, H., Michalakis, S., & Karl, M. (2021) · Human Gene Therapy · doi:10.1089/hum.2020.321 · Cited by 39
“Organoids from the same batch of differentiation were exposed in parallel to wild-type AAV9 39 or novel capsid variants, AAV9.”
Rationally designed AAV2 and AAVrh8R capsids provide improved transduction in the retina and brain
Sullivan, J. A., Stanek, L. M., Lukason, M. J., Bu, J., Osmond, S. R., Barry, E. A., O’Riordan, C. R., Shihabuddin, L. S., Cheng, S. H., & Scaria, A. (2018) · Gene Therapy · doi:10.1038/s41434-018-0017-8 · Cited by 37
Engineering AAV receptor footprints for gene therapy
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Emmanuel, S. N., Smith, J. K., Hsi, J., Tseng, Y.-S., Kaplan, M., Mietzsch, M., Chipman, P. R., Asokan, A., McKenna, R., & Agbandje‐McKenna, M. (2021) · Journal of Virology · doi:10.1128/jvi.01251-21 · Cited by 36
Self-citationLam, A. K., Zhang, J., Frabutt, D. A., Mulcrone, P. L., Li, L., Zeng, L., Herzog, R. W., & Xiao, W. (2022) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2022.09.008 · Cited by 38
An engineered AAV targeting integrin alpha V beta 6 presents improved myotropism across species
Hong, A. V., Suel, L., Petat, E., Dubois, A., Brun, P., Guerchet, N., Veron, P., Poupiot, J., & Richard, I. (2024) · Nature Communications · doi:10.1038/s41467-024-52002-4 · Cited by 43
“Structurally, the VP3 monomer core contains a highly conserved eight-stranded β -barrel motif 11 .”
BackgroundAAV microdystrophin gene replacement therapy for Duchenne muscular dystrophy: progress and prospects
Chwalenia, K., Feng, V.-Y., Hemmer, N., Friedrichsen, H. J., Vorobieva, I., Wood, M. J. A., & Roberts, T. C. (2025) · Gene Therapy · doi:10.1038/s41434-025-00561-6 · Cited by 38
“1B) [78].”
Xie, Q., Spear, J. M., Noble, A. J., Sousa, D. R., Meyer, N., Davulcu, O., Zhang, F., Linhardt, R. J., Stagg, S. M., & Chapman, M. S. (2017) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2017.02.004 · Cited by 36
Sevvana, M., Klose, T., & Rossmann, M. G. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-814515-9.00033-3 · Cited by 37
Structure-guided AAV capsid evolution strategies for enhanced CNS gene delivery
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Fast Retrograde Access to Projection Neuron Circuits Underlying Vocal Learning in Songbirds
Düring, D. N., Dittrich, F., Rocha, M. D., Tachibana, R. O., Mori, C., Okanoya, K., Boehringer, R., Ehret, B., Grewe, B. F., Gerber, S., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108364 · Cited by 37
“The 10-mer insert between positions 587 and 588 (Figure 1A) probably both disrupts HBD’s functionality, as demonstrated by the reduced heparin binding affinity of AAV-retro, and creates a binding surface, which might improve vesicular trafficking or nuclear entry of viral particles (Tervo et al., 2016).”
InfluentialStructural basis of receptor usage by the engineered capsid AAV-PHP.eB
Jang, S., Shen, H. K., Ding, X., Miles, T. F., & Gradinaru, V. (2022) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2022.07.011 · Cited by 35
Peptide ligands for the affinity purification of adeno‐associated viruses from HEK 293 cell lysates
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“Retrospective evaluation of AAV-DJ refinements With publication of the structure of AAV-9 (Dimattia et al., 2012), it was encouraging to see that a loop known as variable region 1, which differed from AAV-2 and AAV-8 by 4 and 6 Å RMS respectively, was now closely matched by the new crystal structure.”
MethodInfluentialStructure comparison of the chimeric AAV2.7m8 vector with parental AAV2
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Self-citationArtificial Intelligence‐Based Approaches for AAV Vector Engineering
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Atomic structure of a rationally engineered gene delivery vector, AAV2. 5
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Self-citationPan, X., Sands, S. A., Yue, Y., Zhang, K., LeVine, S. M., & Duan, D. (2019) · Human Gene Therapy · doi:10.1089/hum.2019.008 · Cited by 29
Biomaterial-Guided Gene Delivery for Musculoskeletal Tissue Repair
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Biswas, M., Marsic, D., Li, N., Zou, C., González‐Aseguinolaza, G., Zolotukhin, I., Kumar, S. R. P., Rana, J., Butterfield, J. S. S., Kondratov, O., et al. (2020) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2020.09.019 · Cited by 28
Self-citationShay, T. F., Jang, S., Brittain, T. J., Chen, X., Walker, B., Tebbutt, C., Fan, Y., Wolfe, D. A., Arokiaraj, C. M., Sullivan, E. E., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52149-0 · Cited by 28
“Thissubsetof particles was further re fi ned to produce a trimer map at 10.0Å resolution, which was used to build a model of the human IL3-AAV9 interaction through manual rigid-body docking of the human IL3 structure (PDB ID: 5UV8) 90 onto the AAV9 trimer (PDB ID: 3UX1) 91 .”
Metadata
- Authors
- DiMattia, M. A., Nam, H.-J., Van Vliet, K., Mitchell, M., Bennett, A., Gurda, B. L., McKenna, R., Olson, N. H., Sinkovits, R. S., Potter, M., Byrne, B. J., Aslanidi, G., Zolotukhin, S., Muzyczka, N., Baker, T. S., & Agbandje-McKenna, M.
- Affiliations
- University of Florida (US)
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
- University of California San Diego (US)
- University of Florida Health (US)
- ORCID
- Venue
- Journal of Virology
- Publisher
- American Society for Microbiology
- Published
- 2012-06-15
- Volume
- 86
- Issue
- 12
- Pages
- 6947-6958
- ISSN
- 0022-538X (ISSN-L)
- 1098-5514
- PMC
- PMC3393551
- OpenAlex
- W2012799865
- Cited by
- 219
- References
- 91
- Citations by year
- 2026: 15 · 2025: 18 · 2024: 17 · 2023: 16 · 2022: 26 · 2021: 23 · 2020: 18 · 2019: 16 · 2018: 15 · 2017: 6 · 2016: 11 · 2015: 9 · 2014: 12 · 2013: 11 · 2012: 4
- FWCI
- 6.94
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Virology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation
- National Institutes of Health (4r37gm033050-27)
- University of California, San Francisco
- National Heart, Lung, and Blood Institute (P01HL059412, P01 HL 59412)
- National Institute of General Medical Sciences (R37GM-033050, R37 GM-33050, DMR-0225180, R01GM082946)
- Division of Materials Research
- National Center for Research Resources (RR-01646, S10RR020016, P41RR001646, P41RR001081)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Health Sciences › Medicine › Infectious Diseases › Parvovirus B19 Infection Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- AAV9, viral tropism, blood-brain barrier penetration, antigenic diversity, 3D reconstruction
- MeSH terms
- Dependovirus, Capsid, Crystallography, X-Ray, Cryoelectron Microscopy, Imaging, Three-Dimensional, Capsid Proteins
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