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

SASDR33 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) of SARS-CoV-2 in HEPES conditions

Nucleoprotein
MWexperimental 16 kDa
MWexpected 15 kDa
VPorod 26 nm3
log I(s) 9.28×10-3 9.28×10-4 9.28×10-5 9.28×10-6
Nucleoprotein small angle scattering data  s, nm-1
ln I(s)
Nucleoprotein Guinier plot ln 9.29×10-3 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: 5.2 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Nucleoprotein PDB (PROTEIN DATA BANK) model

Synchrotron SAXS data from solutions of the N-terminal RNA-binding domain of nucleocapsid protein of SARS-CoV-2 in 25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH 7.2 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 25°C. 2011 successive 0.99 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. 27 sample frames from the SEC peak were selected for averaging using CHROMIXS.

The quoted experimental molecular weight was determined using MALLS/RI measurements. Additional SEC-SAXS (unsubtracted frames) and MALLS/RI data 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