Coupling of polymerase-nucleoprotein-RNA in an influenza virus mini ribonucleoprotein complex

Huiling Kang, Yunxiang Yang, Yixiao Liu, Mingyu Li, Lejin Zhang, Yuqi Lin, Leander Witte, Kuang-Yu Chen, Wenya Song, Zhili Xu, Xiaojing He, Luke W. Guddat, Yu Guo, Liming Yan, Yan Gao, Ervin Fodor (), Zihe Rao () and Zhiyong Lou ()
Additional contact information
Huiling Kang: ShanghaiTech University
Yunxiang Yang: Tsinghua University
Yixiao Liu: Tsinghua University
Mingyu Li: Tsinghua University
Lejin Zhang: University of Science and Technology of China
Yuqi Lin: University of Science and Technology of China
Leander Witte: University of Oxford
Kuang-Yu Chen: University of Oxford
Wenya Song: The Fourth Hospital of Hebei Medical University
Zhili Xu: University of Science and Technology of China
Xiaojing He: Huazhong University of Science and Technology
Luke W. Guddat: The University of Queensland
Yu Guo: Nankai University
Liming Yan: Tsinghua University
Yan Gao: ShanghaiTech University
Ervin Fodor: University of Oxford
Zihe Rao: ShanghaiTech University
Zhiyong Lou: Tsinghua University

Nature Communications, 2025, vol. 16, issue 1, 1-10

Abstract: Abstract Influenza virus ribonucleoprotein complexes (RNPs), composed of the polymerase complex (FluPol), nucleoprotein (NP), and RNA, are essential for replication and transcription. We report atomic-resolution cryo-EM structures of mini-vRNPs in two states: FluPol located inside (State-In) or at the outer rim (State-Out) of the NP–RNA ring. In both states, the 5′ and 3′ termini of vRNA are bound to FluPol as previously reported. One NP (NP-0) contacts PA/PB1 of FluPol and binds the distal double-stranded vRNA promoter, with its D72–K90 loop inserting into the RNA fork; separated strands occupy NP-0 RNA-binding grooves. Grooves from other NPs form a continuous RNA-protective path, consistent with negative-strand RNA virus mechanisms. In State-In, interfaces for FluPol dimerization or Pol II interaction are blocked, but fully exposed in State-Out. These structures reveal detailed FluPol–NP–RNA coupling and suggest a conformational shift in RNPs during the viral life cycle.

Date: 2025
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DOI: 10.1038/s41467-025-64741-z

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