6QX8

Influenza A virus (A/NT/60/1968) polymerase dimer of heterotrimer in complex with 5' cRNA promoter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structures of influenza A virus RNA polymerase offer insight into viral genome replication.

Fan, H.Walker, A.P.Carrique, L.Keown, J.R.Serna Martin, I.Karia, D.Sharps, J.Hengrung, N.Pardon, E.Steyaert, J.Grimes, J.M.Fodor, E.

(2019) Nature 573: 287-290

  • DOI: 10.1038/s41586-019-1530-7
  • Primary Citation of Related Structures:  
    6QNW, 6QPF, 6QPG, 6QWL, 6QX3, 6QX8, 6QXE, 6RR7

  • PubMed Abstract: 
  • Influenza A viruses are responsible for seasonal epidemics, and pandemics can arise from the transmission of novel zoonotic influenza A viruses to humans 1,2 . Influenza A viruses contain a segmented negative-sense RNA genome, which is transcribed and replicated by the viral-RNA-dependent RNA polymerase (FluPol A ) composed of PB1, PB2 and PA subunits 3-5 ...

    Influenza A viruses are responsible for seasonal epidemics, and pandemics can arise from the transmission of novel zoonotic influenza A viruses to humans 1,2 . Influenza A viruses contain a segmented negative-sense RNA genome, which is transcribed and replicated by the viral-RNA-dependent RNA polymerase (FluPol A ) composed of PB1, PB2 and PA subunits 3-5 . Although the high-resolution crystal structure of FluPol A of bat influenza A virus has previously been reported 6 , there are no complete structures available for human and avian FluPol A . Furthermore, the molecular mechanisms of genomic viral RNA (vRNA) replication-which proceeds through a complementary RNA (cRNA) replicative intermediate, and requires oligomerization of the polymerase 7-10 -remain largely unknown. Here, using crystallography and cryo-electron microscopy, we determine the structures of FluPol A from human influenza A/NT/60/1968 (H3N2) and avian influenza A/duck/Fujian/01/2002 (H5N1) viruses at a resolution of 3.0-4.3 Å, in the presence or absence of a cRNA or vRNA template. In solution, FluPol A forms dimers of heterotrimers through the C-terminal domain of the PA subunit, the thumb subdomain of PB1 and the N1 subdomain of PB2. The cryo-electron microscopy structure of monomeric FluPol A bound to the cRNA template reveals a binding site for the 3' cRNA at the dimer interface. We use a combination of cell-based and in vitro assays to show that the interface of the FluPol A dimer is required for vRNA synthesis during replication of the viral genome. We also show that a nanobody (a single-domain antibody) that interferes with FluPol A dimerization inhibits the synthesis of vRNA and, consequently, inhibits virus replication in infected cells. Our study provides high-resolution structures of medically relevant FluPol A , as well as insights into the replication mechanisms of the viral RNA genome. In addition, our work identifies sites in FluPol A that could be targeted in the development of antiviral drugs.


    Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford, UK. ervin.fodor@path.ox.ac.uk.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase acidic proteinA, E716Influenza A virus (A/nt/60/1968(H3N2))Mutation(s): 0 
Gene Names: PA
EC: 3.1
UniProt
Find proteins for P03434 (Influenza A virus (strain A/Northern Territory/60/1968 H3N2))
Explore P03434 
Go to UniProtKB:  P03434
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunitB, F757Influenza A virus (A/nt/60/1968(H3N2))Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
UniProt
Find proteins for P03432 (Influenza A virus (strain A/Northern Territory/60/1968 H3N2))
Explore P03432 
Go to UniProtKB:  P03432
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase basic protein 2C, G759Influenza A virus (A/nt/60/1968(H3N2))Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for P03429 (Influenza A virus (strain A/Northern Territory/60/1968 H3N2))
Explore P03429 
Go to UniProtKB:  P03429
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*AP*GP*CP*AP*AP*AP*AP*GP*CP*AP*GP*A)-3')D, H15Influenza A virus (A/nt/60/1968(H3N2))
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 4.07 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


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

    Revision History  (Full details and data files)

    • Version 1.0: 2019-09-04
      Type: Initial release
    • Version 1.1: 2019-09-18
      Changes: Data collection, Database references
    • Version 1.2: 2019-09-25
      Changes: Data collection, Database references
    • Version 1.3: 2019-10-23
      Changes: Data collection, Other
    • Version 1.4: 2019-11-06
      Changes: Data collection, Refinement description
    • Version 2.0: 2020-11-18
      Changes: Data collection, Polymer sequence