9DTT

Cryo-EM structure of DENV2 NS5 in complex with Stem Loop A (SLA)

Summary for 9DTT

• Entry DOI: 10.2210/pdb9dtt/pdb
• EMDB information: 47165
• Descriptor: RNA-directed RNA polymerase NS5, stem loop A, ZINC ION (3 entities in total)
• Functional Keywords: rna-dependent rna polymerase, flavivirus, dengue, ns5, viral protein-rna complex, viral protein/rna
• Biological source: dengue virus type 2; More
• Total number of polymer chains: 2
• Total formula weight: 128302.42

Authors

Obi, J.O.,Fields, J.K.,Snyder, A.G.,Deredge, D.J. (deposition date: 2024-10-01, release date: 2024-10-23, Last modification date: 2025-01-08)

Primary citation

Obi, J.O.,Kihn, K.C.,McQueen, L.,Fields, J.K.,Snyder, G.A.,Deredge, D.J.
Structural Dynamics of the Dengue Virus Non-structural 5 (NS5) Interactions with Promoter Stem Loop A (SLA).
Biorxiv, 2024

PubMed Abstract: The dengue virus (DENV) NS5 protein plays a central role in dengue viral RNA synthesis which makes it an attractive target for antiviral drug development. DENV NS5 is known to interact with the stem-loop A (SLA) promoter at the 5'-untranslated region (5'-UTR) of the viral genome as a molecular recognition signature for the initiation of negative strand synthesis at the 3' end of the viral genome. However, the conformational dynamics involved in these interactions are yet to be fully elucidated. Our study explores the structural dynamics of NS5 from DENV serotype 2 (DENV2 NS5) in complex with SLA, employing surface plasmon resonance (SPR), hydrogen - deuterium exchange coupled to mass spectrometry (HDX-MS), computational modeling, and cryoEM single particle analysis to delineate the molecular details of their interaction. Our findings indicate that DENV2 NS5 binds SLA in a closed conformation with significant interdomain cooperation between the methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains, a feature integral to the interaction. Our HDX-MS studies reveal SLA-induced conformational changes in both domains of DENV2 NS5, reflecting a potential mechanism for dengue NS5's multifunctional role in viral replication. Lastly, our cryoEM structure provides the first visualization of the DENV2 NS5-SLA complex, confirming a conserved SLA binding mode across DENV serotypes. These insights obtained from our study enhance our understanding of dengue NS5's complex conformational landscape, supporting the potential development of antiviral strategies targeting dengue NS5's conformational states.

PubMed: 39677779
DOI: 10.1101/2024.12.03.626708

Experimental method

ELECTRON MICROSCOPY (3.6 Å)