6NXE | pdb_00006nxe

Cryo-EM Reconstruction of Protease-Activateable Adeno-Associated Virus 9 (AAV9-L001)

• PDB DOI: https://doi.org/10.2210/pdb6NXE/pdb
• EM Map EMD-0535: EMDB EMDataResource

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


• Deposited: 2019-02-08 Released: 2019-03-13 
• Deposition Author(s): Bennett, A.B., Agbandje-Mckenna, M.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Protease-Activatable Adeno-Associated Virus Vector for Gene Delivery to Damaged Heart Tissue.

Guenther, C.M., Brun, M.J., Bennett, A.D., Ho, M.L., Chen, W., Zhu, B., Lam, M., Yamagami, M., Kwon, S., Bhattacharya, N., Sousa, D., Evans, A.C., Voss, J., Sevick-Muraca, E.M., Agbandje-McKenna, M., Suh, J.

(2019) Mol Ther 27: 611-622

• PubMed: 30772143 
• DOI: https://doi.org/10.1016/j.ymthe.2019.01.015
• Primary Citation Related Structures: 
  6NXE


• PubMed Abstract: 
  

  Adeno-associated virus (AAV) has emerged as a promising gene delivery vector because of its non-pathogenicity, simple structure and genome, and low immunogenicity compared to other viruses. However, its adoption as a safe and effective delivery vector for certain diseases relies on altering its tropism to deliver transgenes to desired cell populations. To this end, we have developed a protease-activatable AAV vector, named provector, that responds to elevated extracellular protease activity commonly found in diseased tissue microenvironments. The AAV9-based provector is initially inactive, but then it can be switched on by matrix metalloproteinases (MMP)-2 and -9. Cryo-electron microscopy and image reconstruction reveal that the provector capsid is structurally similar to that of AAV9, with a flexible peptide insertion at the top of the 3-fold protrusions. In an in vivo model of myocardial infarction (MI), the provector is able to deliver transgenes site specifically to high-MMP-activity regions of the damaged heart, with concomitant decreased delivery to many off-target organs, including the liver. The AAV provector may be useful in the future for enhanced delivery of transgenes to sites of cardiac damage.

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Organizational Affiliation: 
• Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA.
Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA.
Department of Biochemistry and Molecular Biology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA.
Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 6767 Bertner Avenue, Houston, TX 77225, USA.
Biological Science Imaging facility (BSIR), Department of Biology, 89 Chieftan Way, Florida State University, Tallahassee, FL 32306, USA.
Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 3,656.35 kDa 
• Atom Count: 258,000 
• Modeled Residue Count: 32,640 
• Deposited Residue Count: 32,640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	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]	544	Adeno-associated virus	Mutation(s): 0  Gene Names: cap
UniProt
Find proteins for Q6JC22 (Adeno-associated virus) Explore Q6JC22  Go to UniProtKB:  Q6JC22

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 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: 2019-03-13 
Deposition Author(s): Bennett, A.B., Agbandje-Mckenna, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R21HL126053, R01HL138126, and R01CA207497

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Refinement description