7UD4

Cryo-EM structure of AAV-PHP.eB

This is a non-PDB format compatible entry.

Summary for 7UD4

• Entry DOI: 10.2210/pdb7ud4/pdb
• EMDB information: 26417 26453
• Descriptor: Capsid protein VP1 (1 entity in total)
• Functional Keywords: gene therapy, aav, capsid, blood-brain barrier, directed evolution, virus
• Biological source: Adeno-associated virus
• Total number of polymer chains: 1
• Total formula weight: 82188.61

Authors

Jang, S.,Shen, H.K.,Ding, X.,Miles, T.F.,Gradinaru, V. (deposition date: 2022-03-18, release date: 2022-09-21, Last modification date: 2024-06-12)

Primary citation

Jang, S.,Shen, H.K.,Ding, X.,Miles, T.F.,Gradinaru, V.
Structural basis of receptor usage by the engineered capsid AAV-PHP.eB.
Mol Ther Methods Clin Dev, 26:343-354, 2022

PubMed Abstract: 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.

PubMed: 36034770
DOI: 10.1016/j.omtm.2022.07.011

Experimental method

ELECTRON MICROSCOPY (2.24 Å)