The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements.

Korn SM, Dhamotharan K, Jeffries CM, Schlundt A, Nat Commun 14(1):3331 (2023) Europe PMC

SASDPK6 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) of SARS-CoV-2 in phosphate conditions

Nucleoprotein
MWexperimental 14 kDa
MWexpected 15 kDa
VPorod 23 nm3
log I(s) 8.25×10-3 8.25×10-4 8.25×10-5 8.25×10-6
Nucleoprotein small angle scattering data  s, nm-1
ln I(s)
Nucleoprotein Guinier plot ln 8.26×10-3 Rg: 1.6 nm 0 (1.6 nm)-2 s2
(sRg)2I(s)/I(0)
Nucleoprotein Kratky plot 1.104 0 √3 sRg
p(r)
Nucleoprotein pair distance distribution function Rg: 1.6 nm 0 Dmax: 6.1 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Nucleoprotein PDB (PROTEIN DATA BANK) model
Synchrotron SAXS data from solutions of N-terminal RNA-binding domain (NTD) of nucleocapsid protein of SARS-CoV-2 in 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH 6.5 were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 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 90.00 μl sample at 4.5 mg/ml was injected at a 0.70 ml/min flow rate onto a GE Superdex 75 Increase 10/300 column at 20°C. 2100 successive 0.995 second frames were collected through the SEC elution. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. 13 sample frames from the SEC peak were selected for averaging using CHROMIXS.

Additional SEC-SAXS data (unsubtracted frames) are made available in the full entry zip archive.

Nucleoprotein (NTD)
Mol. type   Protein
Organism   Severe acute respiratory syndrome coronavirus 2
Olig. state   Monomer
Mon. MW   14.9 kDa
 
UniProt   P0DTC9 (44-180)
Sequence   FASTA
 
PDB ID   6M3M