Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.

Lee J, Worrall LJ, Vuckovic M, Rosell FI, Gentile F, Ton AT, Caveney NA, Ban F, Cherkasov A, Paetzel M, Strynadka NCJ, Nat Commun 11(1):5877 (2020) Europe PMC

SASDJG5 – SARS-CoV-2 Main Protease

3C-like proteinase from SARS-CoV-2 replicase polyprotein 1a
MWexperimental 68 kDa
MWexpected 68 kDa
VPorod 93 nm3
log I(s) 2.03×100 2.03×10-1 2.03×10-2 2.03×10-3
3C-like proteinase from SARS-CoV-2 replicase polyprotein 1a small angle scattering data  s, nm-1
ln I(s)
3C-like proteinase from SARS-CoV-2 replicase polyprotein 1a Guinier plot ln 2.03×100 Rg: 2.7 nm 0 (2.7 nm)-2 s2
(sRg)2I(s)/I(0)
3C-like proteinase from SARS-CoV-2 replicase polyprotein 1a Kratky plot 1.104 0 √3 sRg
Dmax: 8.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
3C-like proteinase from SARS-CoV-2 replicase polyprotein 1a PDB (PROTEIN DATA BANK) model
SAXS data from solutions of SARS-CoV-2 main protease in 50 mM Tris, 1 mM DTT, 1 mM EDTA, pH 7.4 were collected using a Rigaku BioSAXS-2000 instrument (University of British Columbia, Vancouver, Canada) equipped with a HyPix-3000 detector at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.2 and 9.6 mg/ml were measured at 6°C. 12 successive 300 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.

Sample detector distance = UNKNOWN

3C-like proteinase from SARS-CoV-2 replicase polyprotein 1a (MPro)
Mol. type   Protein
Organism   Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
Olig. state   Dimer
Mon. MW   33.8 kDa
 
UniProt   P0DTC1 (3264-3569)
Sequence   FASTA
 
PDB ID   6M03