6QX3

Influenza A virus (A/NT/60/1968) polymerase Hetermotrimer in complex with 3'5' cRNA promoter and Nb8205


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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 <sup>1,2 </sup>. Influenza A viruses contain a segmented negative-sense RNA genome, which is tra ...

    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

    Diamond Light Source, Didcot, UK. jonathan@strubi.ox.ac.uk.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Francis Crick Institute, London, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. jonathan@strubi.ox.ac.uk.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Sir William Dunn School of Pathology, University of Oxford, Oxford, UK. ervin.fodor@path.ox.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nb8205
O
134N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase catalytic subunit
B
757Influenza A virus (strain A/Hong Kong/1/1968 H3N2)Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
Find proteins for Q910D6 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Go to UniProtKB:  Q910D6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A
716Influenza A virus (strain A/Northern Territory/60/1968 H3N2)Mutation(s): 0 
Gene Names: PA
EC: 3.1.-.-
Find proteins for P03434 (Influenza A virus (strain A/Northern Territory/60/1968 H3N2))
Go to UniProtKB:  P03434
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
C
762Influenza A virus (strain A/Northern Territory/60/1968 H3N2)Mutation(s): 0 
Gene Names: PB2
Find proteins for P03429 (Influenza A virus (strain A/Northern Territory/60/1968 H3N2))
Go to UniProtKB:  P03429
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*GP*CP*AP*AP*AP*AP*GP*CP*A)-3')D15Influenza A virus (A/nt/60/1968(H3N2))
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*UP*CP*U)-3')G15Influenza A virus (A/nt/60/1968(H3N2))
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
P
Query on P
D
DNA LINKINGC13 H18 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-11
    Type: Data collection, Other
  • Version 1.2: 2019-09-18
    Type: Data collection, Database references
  • Version 1.3: 2019-09-25
    Type: Data collection, Database references