9VD1

Cryo-EM structure of Dimeric Suv3-ssRNA-AMPPNP complex

Summary for 9VD1

• Entry DOI: 10.2210/pdb9vd1/pdb
• EMDB information: 64973
• Descriptor: RNA (5'-R(P*UP*U)-3'), ATP-dependent RNA helicase SUPV3L1, mitochondrial, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (3 entities in total)
• Functional Keywords: helicase, rna binding protein, hydrolase, hydrolase-rna complex, hydrolase/rna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 172481.52

Authors

Patra, M.,Yuan, H.S. (deposition date: 2025-06-07, release date: 2026-05-20)

Primary citation

Patra, M.,Jain, M.,Li, Y.C.,Chen, Y.P.,Golzarroshan, B.,Yuan, H.S.
Asymmetric dimeric assembly of Suv3 helicase facilitates processive RNA unwinding.
Nat Commun, 2026

PubMed Abstract: Human Suv3 is a dimeric helicase that collaborates with the exoribonuclease PNPase to mediate RNA decay and surveillance in mitochondria. Despite its pivotal role in maintaining mitochondrial homeostasis, the molecular mechanism underlying Suv3-mediated RNA unwinding has remained elusive. Here, we present near-atomic-resolution cryogenic electron microscopy structures of Suv3 captured in four functional states: the apo form, two binary complexes with ADP and single-stranded RNA (ssRNA), and a ternary complex with ssRNA and an ATP analog (AMP-PNP). These structures reveal an unexpected asymmetric dimeric organization, in which only one of the two protomers engages in the initial binding of ADP, ssRNA, or both ssRNA and AMP-PNP. Complementary biochemical analyses demonstrate that Suv3 dimerization significantly enhances RNA-binding and unwinding efficiency in an ATP-hydrolysis-dependent manner. Together, these findings provide key insights into the dimeric architecture of Suv3 and establish a mechanistic framework for its coordinated function in processive RNA unwinding.

PubMed: 41986356
DOI: 10.1038/s41467-026-71901-2

Experimental method

ELECTRON MICROSCOPY (4.16 Å)