Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis and dynamics of Chikungunya alphavirus RNA capping by nsP1 capping pores.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 120, Issue 12, Page e2213934120, Year 2023
Publish date	Mar 21, 2023
Authors	Rhian Jones / Michael Hons / Nadia Rabah / Noelia Zamarreño / Rocío Arranz / Juan Reguera /
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 ...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.
External links	Proc Natl Acad Sci U S A / PubMed:36913573 / PubMed Central
Methods	EM (single particle)
Resolution	2.48 - 3.2 Å
Structure data	15553 8aov EMDB-15553, PDB-8aov: CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with GTP Method: EM (single particle) / Resolution: 2.48 Å 15554 8aow EMDB-15554, PDB-8aow: CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with m7GTP and SAH ligands Method: EM (single particle) / Resolution: 2.7 Å 15555 8aox EMDB-15555, PDB-8aox: CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with SAM Method: EM (single particle) / Resolution: 2.8 Å 15578 8apx EMDB-15578, PDB-8apx: CryoEM structure of the Chikungunya virus nsP1 capping pores in covalent complex with a 7GMP cap structure Method: EM (single particle) / Resolution: 3.2 Å 15704 8axv EMDB-15704, PDB-8axv: Structure of an open form of CHIKV nsP1 capping pores Method: EM (single particle) / Resolution: 2.8 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM / Guanosine triphosphate ChemComp-HOH: WATER / Water ChemComp-SAH: S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine ChemComp-MGP: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE ChemComp-MG: Unknown entry ChemComp-SAM: S-ADENOSYLMETHIONINE / S-Adenosyl methionine ChemComp-MY6*: 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one / 7-Methylguanine
Source	Baculovirus expression vector pFastBac1-HM chikungunya virus strain s27-african prototype
Keywords	VIRAL PROTEIN / Alphavirus Replication complex capping pores membrane pore Methyltransferase Guanylyl transferase / Alphavirus Replication complex Capping pores Membrane pore Methyltransferase gunayltransferase VIRAL PROTEIN / Alphavirus Replication complex / capping pores / membrane pore / Methyltransferase / Guanylyl transferase / VIRAL PROT