8TEX | pdb_00008tex

Avian Adeno-associated virus - empty capsid

• PDB DOI: https://doi.org/10.2210/pdb8TEX/pdb
• EM Map EMD-41208: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Avian adeno-associated virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-07-07 Released: 2023-08-30 
• Deposition Author(s): Hsi, J., Mietzsch, M., Chipman, P., Afione, S., Zeher, A., Huang, R., Chiorini, J., McKenna, R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and antigenic characterization of the avian adeno-associated virus capsid.

Hsi, J., Mietzsch, M., Chipman, P., Afione, S., Zeher, A., Huang, R., Chiorini, J., McKenna, R.

(2023) J Virol 97: e0078023-e0078023

• PubMed: 37702486 
• DOI: https://doi.org/10.1128/jvi.00780-23
• Primary Citation Related Structures: 
  8TEX, 8TEY


• PubMed Abstract: 
  

  AAVs are extensively studied as promising therapeutic gene delivery vectors. In order to circumvent pre-existing antibodies targeting primate-based AAV capsids, the AAAV capsid was evaluated as an alternative to primate-based therapeutic vectors. Despite the high sequence diversity, the AAAV capsid was found to bind to a common glycan receptor, terminal galactose, which is also utilized by other AAVs already being utilized in gene therapy trials. However, contrary to the initial hypothesis, AAAV was recognized by approximately 30% of human sera tested. Structural and sequence comparisons point to conserved epitopes in the fivefold region of the capsid as the reason determinant for the observed cross-reactivity.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida , Gainesville, Florida, USA.
National Institute of Dental and Craniofacial Research, NIH , Bethesda, Maryland, USA.
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, Maryland, USA.
Department of Epidemiology, Bloomberg School for Public Health, Johns Hopkins University , Baltimore, Maryland, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3,614.25 kDa 
• Atom Count: 247,440 
• Modeled Residue Count: 30,720 
• Deposited Residue Count: 32,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, AA [auth a], AB [auth 1], B, BA [auth b], BB [auth 2], C, CA [auth c], CB [auth 3], D, DA [auth d], DB [auth 4], E, EA [auth e], EB [auth 5], F, FA [auth f], FB [auth 6], G, GA [auth g], GB [auth 7], H, HA [auth h], HB [auth 8], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	535	Avian adeno-associated virus	Mutation(s): 0  Gene Names: Cap
UniProt
Find proteins for Q7TG43 (Avian adeno-associated virus) Explore Q7TG43  Go to UniProtKB:  Q7TG43

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-30 
Deposition Author(s): Hsi, J., Mietzsch, M., Chipman, P., Afione, S., Zeher, A., Huang, R., Chiorini, J., McKenna, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH GM082946

Revision History  

• Version 1.0: 2023-08-30
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Database references
• Version 1.3: 2025-05-28
  Changes: Data collection, Structure summary