9V46 | pdb_00009v46

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

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

Kang, H.Yang, Y.Liu, Y.Li, M.Zhang, L.Lin, Y.Witte, L.Chen, K.Y.Song, W.Xu, Z.He, X.Guddat, L.W.Guo, Y.Yan, L.Gao, Y.Fodor, E.Rao, Z.Lou, Z.

(2025) Nat Commun 16: 9741-9741

  • DOI: https://doi.org/10.1038/s41467-025-64741-z
  • Primary Citation of Related Structures:  
    9V44, 9V46, 9V47, 9V48

  • PubMed 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.


  • Organizational Affiliation
    • Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase acidic protein716Influenza A virus (A/Victoria/3/1975(H3N2))Mutation(s): 0 
Gene Names: PA
EC: 3.1
UniProt
Find proteins for H9XIJ2 (Influenza A virus (strain A/Victoria/3/1975 H3N2))
Explore H9XIJ2 
Go to UniProtKB:  H9XIJ2
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UniProt GroupH9XIJ2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunit757Influenza A virus (A/Victoria/3/1975(H3N2))Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for H9XIJ3 (Influenza A virus (strain A/Victoria/3/1975 H3N2))
Explore H9XIJ3 
Go to UniProtKB:  H9XIJ3
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UniProt GroupH9XIJ3
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2759Influenza A virus (A/Victoria/3/1975(H3N2))Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for P31345 (Influenza A virus (strain A/Victoria/3/1975 H3N2))
Explore P31345 
Go to UniProtKB:  P31345
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UniProt GroupP31345
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(P*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')D [auth E]9Influenza A virus (A/Victoria/3/1975(H3N2))
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*UP*G)-3')E [auth F]16Influenza A virus (A/Victoria/3/1975(H3N2))
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references