6EUV

Structure of the midlink and cap-binding domains of influenza A polymerase PB2 subunit with a bound azaindole cap-binding inhibitor (VX-787)

Summary for 6EUV

• Entry DOI: 10.2210/pdb6euv/pdb
• Descriptor: Polymerase basic protein 2, (2S,3S)-3-[[5-fluoranyl-2-(5-fluoranyl-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid, NICKEL (II) ION, ... (4 entities in total)
• Functional Keywords: influenza a polymerase, pb2 subunit, cap-binding domain, cap-binding inhibitor, rna binding protein
• Biological source: Influenza A virus (strain A/Victoria/3/1975 H3N2)
• Cellular location: Virion : P31345
• Total number of polymer chains: 4
• Total formula weight: 132728.42

Authors

Cusack, S.,Lethier, M. (deposition date: 2017-10-31, release date: 2017-12-13, Last modification date: 2025-10-01)

Primary citation

Pflug, A.,Gaudon, S.,Resa-Infante, P.,Lethier, M.,Reich, S.,Schulze, W.M.,Cusack, S.
Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors.
Nucleic Acids Res., 46:956-971, 2018

PubMed Abstract: Influenza polymerase uses short capped primers snatched from nascent Pol II transcripts to initiate transcription of viral mRNAs. Here we describe crystal structures of influenza A and B polymerase bound to a capped primer in a configuration consistent with transcription initiation ('priming state') and show by functional assays that conserved residues from both the PB2 midlink and cap-binding domains are important for positioning the capped RNA. In particular, mutation of PB2 Arg264, which interacts with the triphosphate linkage in the cap, significantly and specifically decreases cap-dependent transcription. We also compare the configuration of the midlink and cap-binding domains in the priming state with their very different relative arrangement (called the 'apo' state) in structures where the potent cap-binding inhibitor VX-787, or a close analogue, is bound. In the 'apo' state the inhibitor makes additional interactions to the midlink domain that increases its affinity beyond that to the cap-binding domain alone. The comparison suggests that the mechanism of resistance of certain mutations that allow virus to escape from VX-787, notably PB2 N510T, can only be rationalized if VX-787 has a dual mode of action, direct inhibition of capped RNA binding as well as stabilization of the transcriptionally inactive 'apo' state.

PubMed: 29202182
DOI: 10.1093/nar/gkx1210

Experimental method

X-RAY DIFFRACTION (2.7 Å)