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	Structures of nucleotide-bound Redondovirus Rep protein link conformation and function.
Journal, issue, pages	PLoS Pathog, Vol. 22, Issue 3, Page e1013997, Year 2026
Publish date	Mar 4, 2026
Authors	Saira Montermoso / Kushol Gupta / Ruth Anne Pumroy / Vera Moiseenkova-Bell / Frederic D Bushman / Gregory D Van Duyne /
PubMed Abstract	Circular Rep-encoding single-stranded DNA (CRESS-DNA) virus Rep proteins are multidomain enzymes that mediate viral DNA rolling-circle replication. Reps nick viral DNA to expose a 3' end for ...Circular Rep-encoding single-stranded DNA (CRESS-DNA) virus Rep proteins are multidomain enzymes that mediate viral DNA rolling-circle replication. Reps nick viral DNA to expose a 3' end for polymerase extension, provide an NTP-dependent helicase activity for DNA unwinding, and join nicked ends to form circular viral genomes. Here, we present the first structures of a Rep protein from the Redondoviridae family, a newly discovered family of human-associated CRESS-DNA viruses that replicates within the oral protozoan Entamoeba gingivalis. Using cryo-EM, we characterized the hexameric structures of a Redondovirus Rep helicase bound with ATPγS, representing the initial ATP-bound state, and with ADP, reflecting the protein state after hydrolysis. The ADP state, but not the ATP state of Rep shows a staircase arrangement of DNA-binding loops that plays a central role in current models for SF3 helicase function. Additionally, we determined a head-to-tail dodecameric structure of ATPγS-bound Rep, in which both the helicase and endonuclease domains are ordered. Conservation of residues involved in stabilizing the dodecamer suggest that this assembly may be functionally relevant for many CRESS-DNA viruses. The positioning of endonuclease domains in the Rep hexamer, combined with our biophysical analyses of Rep oligomerization, provide new insights into Rep function during viral replication.
External links	PLoS Pathog / PubMed:41779823 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.8 - 3.32 Å
Structure data	71784 9pqj EMDB-71784, PDB-9pqj: Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep hexamer Method: EM (single particle) / Resolution: 2.36 Å 71786 9pqm EMDB-71786, PDB-9pqm: Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep hexamer with endonuclease domain density Method: EM (single particle) / Resolution: 3.18 Å 71787 9pqo EMDB-71787, PDB-9pqo: Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep pentamer Method: EM (single particle) / Resolution: 3.1 Å 71788 9pqq EMDB-71788, PDB-9pqq: Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep double hexamer with C1 symmetry Method: EM (single particle) / Resolution: 3.32 Å 71789 9pqr EMDB-71789, PDB-9pqr: Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep double hexamer with C6 symmetry Method: EM (single particle) / Resolution: 2.95 Å 71790 9pqt EMDB-71790, PDB-9pqt: Cryo-EM structure of ADP-bound Vientovirus FB Rep hexamer Method: EM (single particle) / Resolution: 3.2 Å PDB-9pqf: Xray crystal structure of Vientovirus FB Rep endonuclease domain 2-114 with Mg2+ ion Method: X-RAY DIFFRACTION / Resolution: 1.8 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-MLI: MALONATE ION ChemComp-HOH: WATER ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogueYM ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM
Source	Vientovirus FB human lung-associated vientovirus fb
Keywords	REPLICATION / Endonuclease / DNA binding protein / Viral protein / SF3 helicase