9PQM

Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep hexamer with endonuclease domain density

Summary for 9PQM

• Entry DOI: 10.2210/pdb9pqm/pdb
• Related: 9PQF 9PQJ
• EMDB information: 71784 71786
• Descriptor: Replication-associated protein, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER, MAGNESIUM ION (3 entities in total)
• Functional Keywords: sf3 helicase, dna binding protein, replication, viral protein
• Biological source: Human lung-associated vientovirus FB
• Total number of polymer chains: 6
• Total formula weight: 149451.23

Authors

Montermoso, S.,Gupta, K.,Pumroy, R.A.,Moiseenkova-Bell, V.,Bushman, F.D.,Van Duyne, G.D. (deposition date: 2025-07-22, release date: 2026-02-25, Last modification date: 2026-03-18)

Primary citation

Montermoso, S.,Gupta, K.,Pumroy, R.A.,Moiseenkova-Bell, V.,Bushman, F.D.,Van Duyne, G.D.
Structures of nucleotide-bound Redondovirus Rep protein link conformation and function.
Plos Pathog., 22:e1013997-e1013997, 2026

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 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.

PubMed: 41779823
DOI: 10.1371/journal.ppat.1013997

Experimental method

ELECTRON MICROSCOPY (3.18 Å)