9IM6 | pdb_00009im6

Structure of influenza A virus RNA polymerase PB1 and nuclear import host factor RanBP5 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Structural insights into Influenza A virus RNA polymerase PB1 binding to nuclear import host factor RanBP5.

Uchikubo-Kamo, T.Ishimoto, N.Umezawa, H.Hirohama, M.Ono, M.Kawabata, H.Kamata, K.Ohki, M.Yoshida, H.Park, J.H.Tame, J.R.H.Kawaguchi, A.Park, S.Y.

(2024) Biochem Biophys Res Commun 739: 150952-150952

  • DOI: https://doi.org/10.1016/j.bbrc.2024.150952
  • Primary Citation of Related Structures:  
    9IM6

  • PubMed Abstract: 

    The genome of influenza A viruses consists of eight RNA segments that form a heterotrimer, and the viral genome undergoes transcription and replication in the nucleus. Thus, during infection, newly synthesized RNA polymerase subunits must be imported into the nucleus. Although several models have been proposed for this process, the consensus is that the RNA polymerase subunits PB1 and PA form a dimer in the cytoplasm and are transported into the nucleus by Ran binding protein 5 (RanBP5). The PB2 subunit undergoes separate transport to complete the nuclear import. However, the molecular mechanism of nuclear import by host factors and their interactions with proteins are largely unknown. Here we present the structural analysis of the RanBP5 and PB1 NLS domain complex by cryo-EM at 3.2 Å resolution. The pattern shows that the NLS domain of PB1 does not exist in a secondary structure and interacts with RanBP5 in a wrapped state. In addition, biochemical analyses of the mutant have identified critical amino acid sites involved in complex binding. The results suggest a stepwise assembly of influenza virus structural components regulated by nuclear import mechanisms and host factor binding, with important implications for drug discovery research.


  • Organizational Affiliation
    • Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Importin-51,118Homo sapiensMutation(s): 0 
Gene Names: IPO5KPNB3RANBP5
UniProt & NIH Common Fund Data Resources
Find proteins for O00410 (Homo sapiens)
Explore O00410 
Go to UniProtKB:  O00410
PHAROS:  O00410
GTEx:  ENSG00000065150 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00410
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunit53Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for P03431 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03431 
Go to UniProtKB:  P03431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03431
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 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: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection