9RYC | pdb_00009ryc

Structure of human 1918 influenza A polymerase heterotrimer in complex with WSN NEP.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Regulatory hotspot on the influenza A virus polymerase revealed through the structure of the NEP-polymerase complex.

Rep, A.Wang, F.Chen, K.Y.Carrique, L.Sharps, J.Grimes, J.M.Fodor, E.

(2026) Sci Adv 12: eaeb4073-eaeb4073

  • DOI: https://doi.org/10.1126/sciadv.aeb4073
  • Primary Citation of Related Structures:  
    9RVE, 9RYC

  • PubMed Abstract: 

    Influenza A virus (IAV) transcribes and replicates its segmented RNA genome in the host nucleus within viral ribonucleoproteins (vRNPs), which are exported for virion assembly. The nuclear export protein (NEP) is essential for this process and also regulates viral RNA synthesis, implicating a direct interaction with the viral RNA polymerase. Here, we present a 2.5-Å cryogenic electron microscopy structure of NEP bound to the IAV polymerase and demonstrate that NEP alone is sufficient to promote vRNP export, with the viral matrix protein 1 enhancing export efficiency. NEP forms a four-helix bundle that binds at the interface of the PA C-terminal domain and PB1 N terminus of the polymerase. The NEP binding site at this interface overlaps with those for the host ANP32 and the C-terminal domain of RNA polymerase II, indicating that it functions as a regulatory hotspot coordinating transitions of the viral polymerase between RNA synthesis and nuclear export, revealing a critical layer of control in the IAV replication cycle.


  • Organizational Affiliation
    • Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase acidic protein716Influenza A virus (A/Brevig Mission/1/1918(H1N1))Mutation(s): 0 
Gene Names: PA
EC: 3.1
UniProt
Find proteins for Q3HM39 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Explore Q3HM39 
Go to UniProtKB:  Q3HM39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3HM39
Sequence Annotations
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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/Brevig Mission/1/1918(H1N1))Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for Q3HM40 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Explore Q3HM40 
Go to UniProtKB:  Q3HM40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3HM40
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2765Influenza A virus (A/Brevig Mission/1/1918(H1N1))Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for Q3HM41 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Explore Q3HM41 
Go to UniProtKB:  Q3HM41
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UniProt GroupQ3HM41
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear export protein130Influenza A virus (A/Brevig Mission/1/1918(H1N1))Mutation(s): 0 
Gene Names: NS
UniProt
Find proteins for Q77IX1 (Influenza A virus (strain A/Brevig Mission/1/1918 H1N1))
Explore Q77IX1 
Go to UniProtKB:  Q77IX1
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UniProt GroupQ77IX1
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONcryoSPARC4.2 - 4.7

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom200835/Z/16/Z
Wellcome TrustUnited Kingdom222510/Z/21/Z
Medical Research Council (MRC, United Kingdom)United KingdomMR/R009945/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/X008312/1
Wellcome TrustUnited Kingdom093305/Z/10/Z
Wellcome TrustUnited Kingdom060208/Z/00/Z
Wellcome TrustUnited Kingdom203141/Z/16/Z
Wellcome TrustUnited Kingdom227570/Z/23/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-02-04
    Changes: Data collection, Database references, Structure summary