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TitleCryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 3, Year 2025
Publish dateJan 24, 2025
AuthorsRahul Jaiswal / Brandon Braud / Karen C Hernandez-Ramirez / Vishaka Santosh / Alexander Washington / Carlos R Escalante /
PubMed AbstractThe Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 ...The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states. In the nucleotide-free state, Rep68 forms a heptameric complex around DNA, with three origin-binding domains (OBDs) bound to the Rep-binding element sequence, while three remaining OBDs form transient dimers with them. The AAA+ domains form an open ring without interactions between subunits and DNA. We hypothesize that the heptameric structure is crucial for loading Rep68 onto double-stranded DNA. The ATPγS complex shows that only three subunits associate with the nucleotide, leading to a conformational change that promotes the formation of both intersubunit and DNA interactions. Moreover, three phenylalanine residues in the AAA+ domain induce a steric distortion in the DNA. Our study provides insights into how an SF3 helicase assembles on DNA and provides insights into the DNA melting process.
External linksNucleic Acids Res / PubMed:39883011 / PubMed Central
MethodsEM (single particle)
Resolution3.64 - 5.32 Å
Structure data

44424

9bc5

EMDB-44424, PDB-9bc5:
AAV-2 Rep68-AAVS1 heptameric complex
Method: EM (single particle) / Resolution: 5.32 Å

44902

9bu7

EMDB-44902: Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1
PDB-9bu7: Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1: Insights into the mechanism of DNA melting.
Method: EM (single particle) / Resolution: 3.64 Å

Chemicals

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

Source
  • AAV-2 (virus)
  • adeno-associated virus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN/DNA / Adeno-associated virus / non-structural protein / AAVS1 integration site / Protein-DNA complex / VIRAL PROTEIN / VIRAL PROTEIN-DNA complex / AAV / Replication / Helicase / AAA+ / SF3 / DNA BINDING PROTEIN

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