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; Zhiyong Lou

doi:10.1038/s41467-025-64741-z

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

Nat Commun. 2025 Nov 4;16(1):9741. doi: 10.1038/s41467-025-64741-z.

Authors

Huiling Kang^#^{1

2

3

4}, Yunxiang Yang^#², Yixiao Liu^#², Mingyu Li^#², Lejin Zhang^#⁵, Yuqi Lin⁵, Leander Witte⁶, Kuang-Yu Chen⁶, Wenya Song⁷, Zhili Xu⁵, Xiaojing He⁸, Luke W Guddat⁹, Yu Guo¹⁰, Liming Yan², Yan Gao¹, Ervin Fodor¹¹, Zihe Rao^{12

13

14

15

16

17}, Zhiyong Lou^{18

19}

Affiliations

¹ Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
² MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China.
³ Guangzhou National Laboratory, Guangzhou, China.
⁴ Department of Clinical Laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing, China.
⁵ Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
⁶ Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
⁷ Department of Medical Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
⁸ MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
⁹ School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
¹⁰ State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China.
¹¹ Sir William Dunn School of Pathology, University of Oxford, Oxford, UK. ervin.fodor@path.ox.ac.uk.
¹² Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. raozh@tsinghua.edu.cn.
¹³ MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China. raozh@tsinghua.edu.cn.
¹⁴ Guangzhou National Laboratory, Guangzhou, China. raozh@tsinghua.edu.cn.
¹⁵ Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. raozh@tsinghua.edu.cn.
¹⁶ State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China. raozh@tsinghua.edu.cn.
¹⁷ National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. raozh@tsinghua.edu.cn.
¹⁸ MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China. louzy@mail.tsinghua.edu.cn.
¹⁹ State Key Laboratory of Virology, Wuhan, China. louzy@mail.tsinghua.edu.cn.

^# Contributed equally.

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.

MeSH terms

Cryoelectron Microscopy
Humans
Influenza A virus* / genetics
Models, Molecular
Nucleoproteins* / chemistry
Nucleoproteins* / metabolism
Protein Binding
RNA, Viral* / chemistry
RNA, Viral* / genetics
RNA, Viral* / metabolism
RNA, Viral* / ultrastructure
RNA-Binding Proteins / metabolism
RNA-Dependent RNA Polymerase* / chemistry
RNA-Dependent RNA Polymerase* / metabolism
Ribonucleoproteins* / chemistry
Ribonucleoproteins* / metabolism
Ribonucleoproteins* / ultrastructure
Viral Proteins* / chemistry
Viral Proteins* / metabolism
Virus Replication

Substances

RNA, Viral
Ribonucleoproteins
RNA-Dependent RNA Polymerase
Viral Proteins
RNA-Binding Proteins
Nucleoproteins

Abstract

MeSH terms

Substances

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