The DOI matches its Crossref record; 72 of the 76 references it cites were found in a registry or an index.
Heparin binding induces conformational changes in Adeno-associated virus serotype 2
Open accessAbstract
Adeno-associated virus serotype 2 (AAV2) uses heparan sulfate proteoglycan as a cell surface-attachment receptor. In this study the structures of AAV2 alone and complexed with heparin were determined to approximately 18A resolution using cryo-electron microscopy and three-dimensional image reconstruction. A difference map showed positive density, modeled as heparin, close to the icosahedral twofold axes and between the protrusions that surround the threefold axes of the capsid. Regions of the model near the threefold place the receptor in close proximity to basic residues previously identified as part of the heparin binding site. The region of the model near the twofold axes identifies a second contact site, not previously characterized but which is also possibly configured by heparin binding. The difference map also revealed two significant conformational changes: (I) at the tops of the threefold protrusions, which have become flattened in the complex, and (II) at the fivefold axes where the top of the channel is widened possibly in response to movement of the HI loops in the capsid proteins. Ordered density in the interior of the capsid in the AAV2-heparin complex was interpreted as nucleic acid, consistent with the presence of non-viral DNA in the expressed capsids.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“For example, for AAV2, two critical residues required for binding HS, R585 and R588, reside within VR-VIII, and the 511-NGR-513 proposed to play a role in α5β1 co-receptor binding is flanked by VR-I and VR-IV (Asokan et al., 2006; Kern et al., 2003; Levy et al., 2009; Ng et al., 2010; Opie et al., 2003; Shen et al., 2015; Summerford and Samulski, 1998).”
From Structure comparison of the chimeric AAV2.7m8 vector with parental AAV2 (2020) · cites this paper as Levy et al., 2009
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“different types of contaminating DNA sequences have been described as being copackaged with the transgenes, including fragments of the host cell genome from the cells that are used during vector production [81].”
From Understanding Capsid Assembly and Genome Packaging for Adeno-Associated Viruses (2017) · cites this paper as [81]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 46,047
The CCP4 suite: programs for protein crystallography
Number Collaborative Computational Project (1994) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444994003112 · Cited by 17,317
Jones, T. A., Zou, J.-Y., Cowan, S. W., & Kjeldgaard, M. (1991) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767390010224 · Cited by 12,616 · cited 1×
“The two resultant, essentially identical, difference density maps were inspected using Chimera (Pettersen et al., 2004) and O (Jones et al., 1991).”
MethodSafety and Efficacy of Gene Transfer for Leber's Congenital Amaurosis
Maguire, A. M., Simonelli, F., Pierce, E. A., Pugh, E. N., Mingozzi, F., Bennicelli, J., Banfi, S., Marshall, K. A., Testa, F., Surace, E. M., et al. (2008) · New England Journal of Medicine · doi:10.1056/nejmoa0802315 · Cited by 2,145 · cited 1×
“Extrusion and activity of the VP1-N terminal PLA2 domain is essential for efficient infection and is believed to occur during or shortly after virus entry into the cell (Bleker et al., 2005; Farr et al., 2006; Mani et al., 2006; Suikkanen et al., 2003; Vihinen-Ranta et al., 2002).”
BackgroundSummerford, C., & Samulski, R. J. (1998) · Journal of Virology · doi:10.1128/jvi.72.2.1438-1445.1998 · Cited by 1,409 · cited 2×
“Heparan sulfate proteoglycan, the first receptor identified for an AAV virus (Summerford and Samulski, 1998), functions during infection to attach AAV2 and AAV3 to the cell surface.”
BackgroundKay, M. A., Manno, C. S., Ragni, M. V., Larson, P. J., Couto, L. B., McClelland, A., Glader, B. E., Chew, A. K., Tai, S. J., Herzog, R. W., et al. (2000) · Nature Genetics · doi:10.1038/73464 · Cited by 1,019 · cited 7×
“AAV2 residues R484, R487, K527, K532, R585, and R588 have been shown to affect heparin binding in mutagenesis studies (Kern et al., 2003; Opie et al., 2003; Wu et al., 2000).”
BackgroundInfluentialHeparin Structure and Interactions with Basic Fibroblast Growth Factor
Faham, S., Hileman, R. E., Fromm, J. R., Linhardt, R. J., & Rees, D. C. (1996) · Science · doi:10.1126/science.271.5252.1116 · Cited by 798 · cited 2×
“Heparin molecules, extracted from the atomic coordinates of the structure of a heparin hexasaccharide complexed with fibroblast growth factor (FGF- heparin) (Faham et al., 1996) (PDB Accession No.”
BackgroundαVβ5 integrin: a co-receptor for adeno-associated virus type 2 infection
Summerford, C., Bartlett, J. S., & Samulski, R. J. (1999) · Nature Medicine · doi:10.1038/4768 · Cited by 711 · cited 2×
“Efficient AAV2 infection also requires a co-receptor, such as human fibroblast growth factor receptor 1 (FGFR1), integrins avb5 and a5b1, or hepatocyte growth factor receptor (Asokan et al., 2006; Kashiwakura et al., 2005; Summerford et al., 1999; Qing et al., 1999).”
BackgroundSpeir, J. A., Munshi, S. K., Wang, G., Baker, T. S., & Johnson, J. E. (1995) · Structure · doi:10.1016/s0969-2126(01)00135-6 · Cited by 698 · cited 1×
“Bink and Pleij, 2002; Prasad et al., 1994; Speir et al., 1995; Tang et al., 2001).”
Self-citationThe atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy
Xie, Q., Bu, W., Bhatia, S., Hare, J., Somasundaram, T., Azzi, A., & Chapman, M. S. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.162250899 · Cited by 612
Flagged first, then by citations
4 of the 76 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Items 101–110 of 110
The Impact of Peptide Insertions on Adeno-Associated Viral Vector Fate
Uhrig, S. (2010) · Kölner Universitäts PublikationsServer (Universität zu Köln)
Chiorini, J. A. (2016) · Oral Diseases · doi:10.1111/odi.12495
[Capsid assembly and DNA encapsidation of adeno-associated virus].
Qizhao, W., Lü, Y., Li, Z., Diao, Y., & Xu, R. (2011) · PubMed
Nicolson, S. C. (2014) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/gbv4-z740
マルチトーン信号のピーク対平均電力比(PAPR)を低減する初期位相設定法
楢橋, 祥., & 野島, 俊. (1995)
(2009) · Current Opinion in Rheumatology · doi:10.1097/bor.0b013e328334b3e8
Characterisation of AAV capsid-specific CD8+ T cell responses in human subjects
Vandamme, C. (2016) · theses.fr (ABES) · doi:10.70675/371e4bbfze69az417bz960azf9db02287546
Etude de la réponse immunitaire virale préexistante anti-AAV chez l'homme
Xicluna, R. (2019) · theses.fr (ABES) · doi:10.70675/d2f47d7cz4f46z448cz85afz657c9516c86f
Olarewaju, O., Bentler, M., Breuer, J., Alioglu, F., Grabowski, A., Prosche, A., Sami, H., Ogris, M., & Büning, H. (2026) · Human Gene Therapy · doi:10.1177/10430342261465461
“22 Interestingly, cryo-electron microscopy data argue that the N residue is shielded from the surface and might only become accessible through a conformational change of the capsid induced by binding to HSPG. 23 Once in the endosomal compartment, AAV is traf-fi cked toward the nucleus, and this involves at least in par…”
Influential
Metadata
- Authors
- Levy, H. C., Bowman, V. D., Govindasamy, L., McKenna, R., Nash, K., Warrington, K., Chen, W., Muzyczka, N., Yan, X., Baker, T. S., & Agbandje-McKenna, M.
- Affiliations
- University of Florida (US)
- Purdue University West Lafayette (US)
- University of California San Diego (US)
- Venue
- Journal of Structural Biology
- Publisher
- Elsevier BV
- Published
- 2009-03
- Volume
- 165
- Issue
- 3
- Pages
- 146-156
- ISSN
- 1047-8477 (ISSN-L)
- PMC
- PMC3694330
- OpenAlex
- W2156683693
- Cited by
- 110
- References
- 76
- Citations by year
- 2026: 4 · 2025: 1 · 2024: 2 · 2023: 3 · 2022: 3 · 2021: 8 · 2020: 3 · 2019: 10 · 2018: 2 · 2017: 5 · 2016: 7 · 2015: 8 · 2014: 10 · 2013: 11 · 2012: 10
- FWCI
- 4.13
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Journal of Structural Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (4r37gm033050-27)
- National Heart, Lung, and Blood Institute (P01HL059412, P01HL051811)
- National Institute of General Medical Sciences (R37GM-033050)
- National Institute of Allergy and Infectious Diseases (P01AI045976)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Keywords
- AAV2, heparin binding, capsid conformational change, heparan sulfate proteoglycans, capsid structure
- MeSH terms
- Dependovirus, Capsid, Heparin, Image Processing, Computer-Assisted, Models, Molecular, Protein Conformation, Virion, Mutagenesis, Site-Directed, Nucleocapsid, Cryoelectron Microscopy, Capsid Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
