9B52 | pdb_00009b52

RhAAV4282 Empty Capsid

• PDB DOI: https://doi.org/10.2210/pdb9B52/pdb
• EM Map EMD-44196: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Adeno-associated virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-03-22 Released: 2024-11-13 
• Deposition Author(s): Dagotto, G., Jenni, S., Li, Z., Barouch, D.H.
• Funding Organization(s): National Institutes of Health/Office of the Director

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.57 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Identification of a novel neutralization epitope in rhesus AAVs.

Dagotto, G., Fisher, J.L., Li, D., Li, Z., Jenni, S., Li, Z., Tartaglia, L.J., Abbink, P., Barouch, D.H.

(2024) Mol Ther Methods Clin Dev 32: 101350-101350

• PubMed: 39469420 
• DOI: https://doi.org/10.1016/j.omtm.2024.101350
• Primary Citation Related Structures: 
  9B52, 9B53


• PubMed Abstract: 
  

  Adeno-associated viruses (AAVs) are popular gene therapy delivery vectors, but their application can be limited by anti-vector immunity. Both preexisting neutralizing antibodies (NAbs) and post-administration NAbs can limit transgene expression and reduce the clinical utility of AAVs. The development of novel AAVs will advance our understanding of AAV immunity and may also have practical applications. In this study, we identified five novel AAV capsids from rhesus macaques. RhAAV4282 exhibited 91.4% capsid sequence similarity with AAV7 and showed similar tissue tropism with slightly diminished overall signal. Despite this sequence homology, RhAAV4282 and AAV7 showed limited cross-neutralization. We determined a cryo-EM structure of the RhAAV4282 capsid at 2.57 Å resolution and identified a small segment within the hypervariable region IV, involving seven amino acids that formed a shortened external loop in RhAAV4282 compared with AAV7. We generated RhAAV4282 and AAV7 mutants that involved swaps of this region and showed that this region partially determined neutralization phenotype. We termed this region the hypervariable region IV neutralizing epitope (HRNE). Our data suggests that modification of the HRNE can lead to AAVs with altered neutralization profiles.

---

Organizational Affiliation: 
• Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.
Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA.
Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 58.14 kDa 
• Atom Count: 4,109 
• Modeled Residue Count: 514 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A [auth 22]	514	Adeno-associated virus	Mutation(s): 0
UniProt
Find proteins for B4Y879 (Adeno-associated virus) Explore B4Y879  Go to UniProtKB:  B4Y879

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.57 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Dagotto, G., Jenni, S., Li, Z., Barouch, D.H.

---

Funding Organization	Location	Grant Number
National Institutes of Health/Office of the Director	United States	OD011170

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release