9IM2

The Cryo-EM structure of MPXV E5 in complex with ssDNA in intermediate state 3

Summary for 9IM2

• Entry DOI: 10.2210/pdb9im2/pdb
• EMDB information: 60680
• Descriptor: Primase D5, DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3'), ADENOSINE MONOPHOSPHATE, ... (6 entities in total)
• Functional Keywords: complex, viral protein/dna, viral protein-dna complex
• Biological source: Monkeypox virus; More
• Total number of polymer chains: 7
• Total formula weight: 547311.34

Authors

Cheng, Y.X.,Han, P.,Wang, H. (deposition date: 2024-07-01, release date: 2025-06-18)

Primary citation

Cheng, Y.,Han, P.,Peng, Q.,Liu, R.,Liu, H.,Yuan, B.,Zhao, Y.,Kuai, L.,Qi, J.,Miao, K.,Shi, Y.,Gao, G.F.,Wang, H.
Assembly and breakage of head-to-head double hexamer reveals mpox virus E5-catalyzed DNA unwinding initiation.
Nat Commun, 16:5176-5176, 2025

PubMed Abstract: The replicative helicase-catalyzed unwinding of the DNA double helix is the initiation of DNA replication. Helicases and primases are functionally related enzymes that have even been expressed as fusion proteins in some organisms and viruses. However, the mechanism underlying DNA unwinding initiation by these helicase-primase fusion enzymes and the functional association between domains have not been elucidated. Herein, we report the cryo-EM structures of mpox virus E5, the founding member of these helicase-primase enzymes, in various enzymatic stages. Notably, E5 forms a head-to-head double hexamer encircling dsDNA, disrupted by the conformational rearrangement of primase domains upon nucleotide incorporation. Five E5-ssDNA-ATP structures further support an ATP cycle-driven non-classical escort model for E5 translocation. Finally, the helicase domain is found to enhance the primase function as a DNA scaffold. Together, our data shed light on the E5-mediated DNA unwinding model including dsDNA loading, DNA melting, ssDNA translocation, and provide a reasonable interpretation for evolutionary preservation of helicase-primase fusion from a functional perspective.

PubMed: 40467608
DOI: 10.1038/s41467-025-60539-1

Experimental method

ELECTRON MICROSCOPY (3.12 Å)