7NIL

1918 H1N1 Viral influenza polymerase heterotrimer with Nb8190 core


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Mapping inhibitory sites on the RNA polymerase of the 1918 pandemic influenza virus using nanobodies.

Keown, J.R.Zhu, Z.Carrique, L.Fan, H.Walker, A.P.Serna Martin, I.Pardon, E.Steyaert, J.Fodor, E.Grimes, J.M.

(2022) Nat Commun 13: 251-251

  • DOI: https://doi.org/10.1038/s41467-021-27950-w
  • Primary Citation of Related Structures:  
    7NFQ, 7NFR, 7NFT, 7NHA, 7NHC, 7NHX, 7NI0, 7NIK, 7NIL, 7NIR, 7NIS, 7NJ3, 7NJ4, 7NJ5, 7NJ7, 7NK1, 7NK2, 7NK4, 7NK6, 7NK8, 7NKA, 7NKC, 7NKI, 7NKR

  • PubMed Abstract: 

    Influenza A viruses cause seasonal epidemics and global pandemics, representing a considerable burden to healthcare systems. Central to the replication cycle of influenza viruses is the viral RNA-dependent RNA polymerase which transcribes and replicates the viral RNA genome. The polymerase undergoes conformational rearrangements and interacts with viral and host proteins to perform these functions. Here we determine the structure of the 1918 influenza virus polymerase in transcriptase and replicase conformations using cryo-electron microscopy (cryo-EM). We then structurally and functionally characterise the binding of single-domain nanobodies to the polymerase of the 1918 pandemic influenza virus. Combining these functional and structural data we identify five sites on the polymerase which are sensitive to inhibition by nanobodies. We propose that the binding of nanobodies at these sites either prevents the polymerase from assuming particular functional conformations or interactions with viral or host factors. The polymerase is highly conserved across the influenza A subtypes, suggesting these sites as effective targets for potential influenza antiviral development.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.


Macromolecules

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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
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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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2,Immunoglobulin G-binding protein A905Influenza A virus (A/Brevig Mission/1/1918(H1N1))Staphylococcus aureus
This entity is chimeric
Mutation(s): 0 
Gene Names: PB2spa
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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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3HM41
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody8190 core133Camelidae mixed libraryMutation(s): 0 
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3')D [auth E]17Influenza A virus (A/Brevig Mission/1/1918(H1N1))
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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*CP*C)-3')E [auth D]15Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom200835/Z/16/Z
Medical Research Council (MRC, United Kingdom)United KingdomMR/R009945/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/K000241/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references