6XB8

Adeno-Associated Virus Origin Binding Domain in complex with ssDNA

Summary for 6XB8

• Entry DOI: 10.2210/pdb6xb8/pdb
• Descriptor: Protein Rep68, DNA (5'-D(*GP*CP*TP*CP*TP*T)-3'), ZINC ION (3 entities in total)
• Functional Keywords: aav, protein-dna, aaa+, sf3, huh, viral protein
• Biological source: Adeno-associated virus 2 (isolate Srivastava/1982) (AAV-2); More
• Total number of polymer chains: 6
• Total formula weight: 99428.68

Authors

Escalante, C.R.,Musayev, F.N. (deposition date: 2020-06-05, release date: 2020-12-09, Last modification date: 2023-10-18)

Primary citation

Santosh, V.,Musayev, F.N.,Jaiswal, R.,Zarate-Perez, F.,Vandewinkel, B.,Dierckx, C.,Endicott, M.,Sharifi, K.,Dryden, K.,Henckaerts, E.,Escalante, C.R.
The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states.
Nucleic Acids Res., 48:12983-12999, 2020

PubMed Abstract: The adeno-associated virus (AAV) non-structural Rep proteins catalyze all the DNA transactions required for virus viability including, DNA replication, transcription regulation, genome packaging, and during the latent phase, site-specific integration. Rep proteins contain two multifunctional domains: an Origin Binding Domain (OBD) and a SF3 helicase domain (HD). Studies have shown that Rep proteins have a dynamic oligomeric behavior where the nature of the DNA substrate molecule modulates its oligomeric state. In the presence of ssDNA, Rep68 forms a large double-octameric ring complex. To understand the mechanisms underlying AAV Rep function, we investigated the cryo-EM and X-ray structures of Rep68-ssDNA complexes. Surprisingly, Rep68 generates hybrid ring structures where the OBD forms octameric rings while the HD forms heptamers. Moreover, the binding to ATPγS promotes a large conformational change in the entire AAA+ domain that leads the HD to form both heptamer and hexamers. The HD oligomerization is driven by an interdomain linker region that acts as a latch to 'catch' the neighboring HD subunit and is flexible enough to permit the formation of different stoichiometric ring structures. Overall, our studies show the structural basis of AAV Rep's structural flexibility required to fulfill its multifunctional role during the AAV life cycle.

PubMed: 33270897
DOI: 10.1093/nar/gkaa1133

Experimental method

X-RAY DIFFRACTION (3.3 Å)