A Caltech Library Service

Structural basis of receptor usage by the engineered capsid AAV-PHP.eB

Jang, Seongmin and Shen, Hao K. and Ding, Xiaozhe and Miles, Timothy F. and Gradinaru, Viviana (2022) Structural basis of receptor usage by the engineered capsid AAV-PHP.eB. Molecular Therapy - Methods & Clinical Development, 26 . pp. 343-354. ISSN 2329-0501. doi:10.1016/j.omtm.2022.07.011.

[img] PDF - Published Version
Creative Commons Attribution Non-commercial No Derivatives.

[img] PDF (Figures S1–S4 and Tables S1 and S2) - Supplemental Material
Creative Commons Attribution Non-commercial No Derivatives.


Use this Persistent URL to link to this item:


Adeno-associated virus serotype 9 (AAV9) is a promising gene therapy vector for treating neurodegenerative diseases due to its ability to penetrate the blood-brain barrier. PHP.eB was engineered from AAV9 by insertion of a 7-amino acid peptide and point mutation of neighboring residues, thereby enhancing potency in the central nervous system. Here, we report a 2.24-Å resolution cryo-electron microscopy structure of PHP.eB, revealing conformational differences from other 7-mer insertion capsid variants. In PHP.eB, the 7-mer loop adopts a bent conformation, mediated by an interaction between engineered lysine and aspartate residues. Further, we identify PKD2 as the main AAV receptor (AAVR) domain recognizing both AAV9 and PHP.eB and find that the PHP.eB 7-mer partially destabilizes this interaction. Analysis of previously reported AAV structures together with our pull-down data demonstrate that the 7-mer topology determined by the lysine-aspartate interaction dictates AAVR binding strength. Our results suggest that PHP.eB’s altered tropism may arise from both an additional interaction with LY6A and weakening of its AAVR interaction. Changing the insertion length, but not sequence, modifies PKD2 binding affinity, suggesting that a steric clash impedes AAVR binding. This research suggests improved library designs for future AAV selections to identify non-LY6A-dependent vectors and modulate AAVR interaction strength.

Item Type:Article
Related URLs:
URLURL TypeDescription Information
Ding, Xiaozhe0000-0002-0267-0791
Miles, Timothy F.0000-0001-6591-3271
Gradinaru, Viviana0000-0001-5868-348X
Additional Information:© 2022 The Author(s). Published by Elsevier. This is an open access article under the CC BY-NC-ND license ( Received 29 April 2022, Accepted 15 July 2022, Available online 31 July 2022. We sincerely thank the staff of the Caltech CLARITY, Optogenetics, & Vector Engineering Center (CLOVER), and members of the Gradinaru lab, especially Josette Medicielo and Zhe Qu, for their help with virus purification, and Catherine Oikonomou for help editing the manuscript. Cryo-EM was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. We especially thank Songye Chen for assisting with cryo-EM data collection. We are grateful to all members of and particularly Sebastien Santini (CNRS/AMU IGS UMR7256) and the PACA BioInfo platform (supported by IBiSA) for the availability and management of This work is supported by a grant from the National Institutes of Health (NIH) to V.G. (NIH Pioneer DP1OD025535). Figure 3A was created with Author contributions: S.J., T.F.M., and V.G. conceived the idea, and V.G. supervised this project. S.J. determined the cryo-EM structures. S.J. and H.K.S. purified the capsids and proteins. S.J. and H.K.S. conducted the pull-down assays. X.D. conducted the RosettaRemodel prediction. S.J., T.F.M., and V.G. wrote the manuscript, and all authors reviewed the data and manuscript. The authors declare no competing interests. Data availability statement: Cryo-EM map and 3D coordinates are available in wwPDB and EMDB with the following accession codes: I1 symmetry applied AAV-PHP.eB, PDB: 7UD4 and EMD: 26453 and symmetry-free AAV-PHP.eB, EMD: 26417.
Funding AgencyGrant Number
Subject Keywords:Adeno-associated virus; AAV; AAVR; LY6A; PHP.eB; blood-brain barrier; cryo-electron microscopy
Record Number:CaltechAUTHORS:20220801-544880000
Persistent URL:
Official Citation:Seongmin Jang, Hao K. Shen, Xiaozhe Ding, Timothy F. Miles, Viviana Gradinaru, Structural basis of receptor usage by the engineered capsid AAV-PHP.eB, Molecular Therapy - Methods & Clinical Development, Volume 26, 2022, Pages 343-354, ISSN 2329-0501,
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:115989
Deposited By: George Porter
Deposited On:01 Aug 2022 22:59
Last Modified:17 Aug 2022 19:40

Repository Staff Only: item control page