Journal Article

Crystal structure of the RNA-dependent RNA polymerase from influenza C virus

Rambo, Robert P., Hengrung, Narin, Fodor, Ervin, El Omari, Kamel, Cusack, Stephen, Stuart, David I., Bricogne, Gérard, Serna Martin, Itziar, Vonrhein, Clemens, Grimes, Jonathan M., Vreede, Frank T.

2015

Overview

The X-ray crystal structure of influenza C virus polymerase, captured in a closed, pre-activation confirmation, is solved at 3.9 Å resolution; comparison with previous RNA-bound structures reveals large conformational changes associated with RNA binding and activation, and illustrates the notable flexibility of the influenza virus RNA polymerase. Atomic structure of influenza C virus RNA polymerase Erwin Fodor and colleagues report the crystal structure of influenza C virus RNA polymerase, captured in a closed, pre-activation conformation. This closed conformation appears very different from previously reported crystal structures of influenza A and B virus polymerases, which contained the RNA promoter. Influenza C infects pigs and humans, but is rarer than the A and B viruses and causes a less severe form of flu. Comparison of the new structure with the previous RNA-bound structures identifies large conformational changes associated with RNA binding and activation, illustrating the flexibility of the influenza virus RNA polymerase. Negative-sense RNA viruses, such as influenza, encode large, multidomain RNA-dependent RNA polymerases that can both transcribe and replicate the viral RNA genome 1 . In influenza virus, the polymerase (FluPol) is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching 2 . Replication occurs through de novo initiation and involves a complementary RNA intermediate. Currently available structures of the influenza A and B virus polymerases include promoter RNA (the 5′ and 3′ termini of viral genome segments), showing FluPol in transcription pre-initiation states 3 , 4 . Here we report the structure of apo-FluPol from an influenza C virus, solved by X-ray crystallography to 3.9 Å, revealing a new ‘closed’ conformation. The apo-FluPol forms a compact particle with PB1 at its centre, capped on one face by PB2 and clamped between the two globular domains of P3. Notably, this structure is radically different from those of promoter-bound FluPols 3 , 4 . The endonuclease domain of P3 and the domains within the carboxy-terminal two-thirds of PB2 are completely rearranged. The cap-binding site is occluded by PB2, resulting in a conformation that is incompatible with transcription initiation. Thus, our structure captures FluPol in a closed, transcription pre-activation state. This reveals the conformation of newly made apo-FluPol in an infected cell, but may also apply to FluPol in the context of a non-transcribing ribonucleoprotein complex. Comparison of the apo-FluPol structure with those of promoter-bound FluPols allows us to propose a mechanism for FluPol activation. Our study demonstrates the remarkable flexibility of influenza virus RNA polymerase, and aids our understanding of the mechanisms controlling transcription and genome replication.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/326/596/1578 / 631/535/1266 / Apoenzymes - chemistry / Apoenzymes - metabolism / Binding Sites / Crystal structure / Crystallography / Crystallography, X-Ray / Crystals / Endonucleases - chemistry / Endonucleases - metabolism / Enzyme Activation / Gammainfluenzavirus - enzymology / Genetic aspects / Humanities and Social Sciences / Influenza / Influenza viruses / letter / Microbiological research / Models, Molecular / multidisciplinary / Peptide Chain Initiation, Translational / Physiological aspects / Promoter Regions, Genetic - genetics / Protein Binding / Protein Structure, Tertiary / Protein Subunits - chemistry / Protein Subunits - metabolism / Ribonucleoproteins - chemistry / RNA Caps - metabolism / RNA polymerase / RNA polymerases / RNA, Viral - biosynthesis / RNA, Viral - metabolism / RNA-Dependent RNA Polymerase - chemistry / RNA-Dependent RNA Polymerase - metabolism / Science / Structure