8AOX

CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with SAM

This is a non-PDB format compatible entry.

Summary for 8AOX

• Entry DOI: 10.2210/pdb8aox/pdb
• Related: 6Z0U
• EMDB information: 15555
• Descriptor: mRNA-capping enzyme nsP1, ZINC ION, S-ADENOSYLMETHIONINE, ... (4 entities in total)
• Functional Keywords: alphavirus replication complex capping pores membrane pore methyltransferase gunayltransferase viral protein, viral protein
• Biological source: Chikungunya virus strain S27-African prototype
• Total number of polymer chains: 24
• Total formula weight: 1450542.43

Authors

Jones, R.,Hons, M.,Reguera, J. (deposition date: 2022-08-08, release date: 2023-03-29, Last modification date: 2024-07-24)

Primary citation

Jones, R.,Hons, M.,Rabah, N.,Zamarreno, N.,Arranz, R.,Reguera, J.
Structural basis and dynamics of Chikungunya alphavirus RNA capping by nsP1 capping pores.
Proc.Natl.Acad.Sci.USA, 120:e2213934120-e2213934120, 2023

PubMed Abstract: Alphaviruses are emerging positive-stranded RNA viruses which replicate and transcribe their genomes in membranous organelles formed in the cell cytoplasm. The nonstructural protein 1 (nsP1) is responsible for viral RNA capping and gates the replication organelles by assembling into monotopic membrane-associated dodecameric pores. The capping pathway is unique to Alphaviruses; beginning with the N methylation of a guanosine triphosphate (GTP) molecule, followed by the covalent linkage of an mGMP group to a conserved histidine in nsP1 and the transfer of this cap structure to a diphosphate RNA. Here, we provide structural snapshots of different stages of the reaction pathway showing how nsP1 pores recognize the substrates of the methyl-transfer reaction, GTP and S-adenosyl methionine (SAM), how the enzyme reaches a metastable postmethylation state with SAH and mGTP in the active site, and the subsequent covalent transfer of mGMP to nsP1 triggered by the presence of RNA and postdecapping reaction conformational changes inducing the opening of the pore. In addition, we biochemically characterize the capping reaction, demonstrating specificity for the RNA substrate and the reversibility of the cap transfer resulting in decapping activity and the release of reaction intermediates. Our data identify the molecular determinants allowing each pathway transition, providing an explanation for the need for the SAM methyl donor all along the pathway and clues about the conformational rearrangements associated to the enzymatic activity of nsP1. Together, our results set ground for the structural and functional understanding of alphavirus RNA-capping and the design of antivirals.

PubMed: 36913573
DOI: 10.1073/pnas.2213934120

Experimental method

ELECTRON MICROSCOPY (2.8 Å)