Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states.
Journal, issue, pages	Nucleic Acids Res, Vol. 48, Issue 22, Page 12983-12999, Year 2020
Publish date	Dec 16, 2020
Authors	Vishaka Santosh / Faik N Musayev / Rahul Jaiswal / Francisco Zárate-Pérez / Bram Vandewinkel / Caroline Dierckx / Molly Endicott / Kamyar Sharifi / Kelly Dryden / Els Henckaerts / Carlos R Escalante /
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 ...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.
External links	Nucleic Acids Res / PubMed:33270897 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	3.3 - 6.7 Å
Structure data	22451 7jse EMDB-22451, PDB-7jse: Adeno-Associated Virus Origin Binding Domain in complex with ssDNA Method: EM (single particle) / Resolution: 4.6 Å 22452 7jsf EMDB-22452, PDB-7jsf: Adeno-Associated Virus Helicase domain Heptamer with ssDNA Method: EM (single particle) / Resolution: 6.7 Å 22453 7jsg EMDB-22453: Adeno-Associated Virus 2 Rep68 HD Hexamer-ssDNA with ATPgS PDB-7jsg: Adeno-Associated Virus 2 Rep68 HD-Heptamer-ssDNA with ATPgS Method: EM (single particle) / Resolution: 5.2 Å 22454 7jsh EMDB-22454, PDB-7jsh: Adeno-Associated Virus 2 Rep68 HD Heptamer-ssAAVS1 with ATPgS Method: EM (single particle) / Resolution: 4.4 Å 22455 7jsi EMDB-22455, PDB-7jsi: Adeno-Associated Virus 2 Rep68 HD Hexamer-ssDNA with ATPgS Method: EM (single particle) / Resolution: 5.01 Å PDB-6xb8: Adeno-Associated Virus Origin Binding Domain in complex with ssDNA Method: X-RAY DIFFRACTION / Resolution: 3.3 Å
Chemicals	ChemComp-ZN: Unknown entry
Source	adeno-associated virus - 2 synthetic construct (others) adeno-associated virus 2 (isolate srivastava/1982)
Keywords	VIRAL PROTEIN / AAV / Protein-DNA / AAA+ / SF3 / HUH / VIRAL PROTEIN/DNA / VIRAL PROTEIN-DNA complex