A SEC-SAXS analysis of SARS-CoV-2 nsp14 apo or in complex with vhh and/or nsp10

Pierre Gauffre.

SASDVV8 – nsp14 and nsp10 from SARS-CoV-2

Replicase polyprotein 1ab (Guanine-N7 methyltransferase nsp14)
Replicase polyprotein 1ab (Non-structural protein 10)
MWI(0) 56 kDa
MWexpected 77 kDa
VPorod 85 nm3
log I(s) 1.42×10-2 1.42×10-3 1.42×10-4 1.42×10-5
Replicase polyprotein 1ab (Guanine-N7 methyltransferase nsp14) Replicase polyprotein 1ab (Non-structural protein 10) small angle scattering data  s, nm-1
ln I(s)
Replicase polyprotein 1ab (Guanine-N7 methyltransferase nsp14) Replicase polyprotein 1ab (Non-structural protein 10) Guinier plot ln 1.43×10-2 Rg: 3.2 nm 0 (3.2 nm)-2 s2
(sRg)2I(s)/I(0)
Replicase polyprotein 1ab (Guanine-N7 methyltransferase nsp14) Replicase polyprotein 1ab (Non-structural protein 10) Kratky plot 1.104 0 √3 sRg
p(r)
Replicase polyprotein 1ab (Guanine-N7 methyltransferase nsp14) Replicase polyprotein 1ab (Non-structural protein 10) pair distance distribution function Rg: 3.3 nm 0 Dmax: 12.3 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Replicase polyprotein 1ab (Guanine-N7 methyltransferase nsp14) Replicase polyprotein 1ab (Non-structural protein 10) DAMMIF model

log I(s)
 s, nm-1
Replicase polyprotein 1ab (Guanine-N7 methyltransferase nsp14) Replicase polyprotein 1ab (Non-structural protein 10) DAMMIN model

Synchrotron SAXS data from solutions of nsp14 and nsp10 from SARS-CoV-2 in 25 mM HEPES, 300 mM NaCl, 5 mM CaCl2, pH 8 were collected on the SWING beam line at the SOLEIL storage ring (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.103316 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 70.00 μl sample at 8.6 mg/ml was injected at a 0.30 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 20°C. 800 successive 0.990 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.

Synchrotron SAXS data from solutions of nsp14 and nsp10 from SARS-CoV-2 in 25 mM HEPES, 300 mM NaCl, 5 mM CaCl2, pH 8 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.103316 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 70.00 μl sample at 8.6 mg/ml was injected at a 0.30 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 20°C. 800 successive 0.990 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.

Replicase polyprotein 1ab (Guanine-N7 methyltransferase nsp14) (Nsp14)
Mol. type   Protein
Organism   Severe acute respiratory syndrome coronavirus 2
Olig. state   Monomer
Mon. MW   59.8 kDa
 
UniProt   P0DTD1 (5926-6452)
Sequence   FASTA
 
Replicase polyprotein 1ab (Non-structural protein 10) (Nsp10)
Mol. type   Protein
Organism   Severe acute respiratory syndrome coronavirus 2
Olig. state   Monomer
Mon. MW   17.2 kDa
 
UniProt   P0DTD1 (4254-4392)
Sequence   FASTA