5IPK

Structure of the R432A variant of Adeno-associated virus type 2 VLP

This is a non-PDB format compatible entry.

Summary for 5IPK

• Entry DOI: 10.2210/pdb5ipk/pdb
• Related: 5IPI
• EMDB information: 8099 8100
• Descriptor: Capsid protein VP1 (1 entity in total)
• Functional Keywords: adeno-associated virus, r432a, gene therapy, icosahedral, dependoparvovirus, virus like particle
• Biological source: Adeno-associated virus - 2 (AAV-2)
• Total number of polymer chains: 60
• Total formula weight: 4916714.04

Authors

Drouin, L.M.,Lins, B.,Janssen, M.E.,Bennet, A.,Chipman, P.,McKenna, R.,Chen, W.,Muzyczka, N.,Cardone, G.,Baker, T.S.,Agbandje-McKenna, M. (deposition date: 2016-03-09, release date: 2016-07-20, Last modification date: 2025-06-04)

Primary citation

Drouin, L.M.,Lins, B.,Janssen, M.,Bennett, A.,Chipman, P.,McKenna, R.,Chen, W.,Muzyczka, N.,Cardone, G.,Baker, T.S.,Agbandje-McKenna, M.
Cryo-electron Microscopy Reconstruction and Stability Studies of the Wild Type and the R432A Variant of Adeno-associated Virus Type 2 Reveal that Capsid Structural Stability Is a Major Factor in Genome Packaging.
J.Virol., 90:8542-8551, 2016

PubMed Abstract: The adeno-associated viruses (AAV) are promising therapeutic gene delivery vectors and better understanding of their capsid assembly and genome packaging mechanism is needed for improved vector production. Empty AAV capsids assemble in the nucleus prior to genome packaging by virally encoded Rep proteins. To elucidate the capsid determinants of this process, structural differences between wild-type (wt) AAV2 and a packaging deficient variant, AAV2-R432A, were examined using cryo-electron microscopy and three-dimensional image reconstruction both at an ∼5.0-Å resolution (medium) and also at 3.8- and 3.7-Å resolutions (high), respectively. The high resolution structures showed that removal of the arginine side chain in AAV2-R432A eliminated hydrogen bonding interactions, resulting in altered intramolecular and intermolecular interactions propagated from under the 3-fold axis toward the 5-fold channel. Consistent with these observations, differential scanning calorimetry showed an ∼10°C decrease in thermal stability for AAV2-R432A compared to wt-AAV2. In addition, the medium resolution structures revealed differences in the juxtaposition of the less ordered, N-terminal region of their capsid proteins, VP1/2/3. A structural rearrangement in AAV2-R432A repositioned the βA strand region under the icosahedral 2-fold axis rather than antiparallel to the βB strand, eliminating many intramolecular interactions. Thus, a single amino acid substitution can significantly alter the AAV capsid integrity to the extent of reducing its stability and possibly rendering it unable to tolerate the stress of genome packaging. Furthermore, the data show that the 2-, 3-, and 5-fold regions of the capsid contributed to producing the packaging defect and highlight a tight connection between the entire capsid in maintaining packaging efficiency.

PubMed: 27440903
DOI: 10.1128/JVI.00575-16

Experimental method

ELECTRON MICROSCOPY (3.7 Å)