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 Jun 7)

PMID: 37286558 doi: 10.1038/s41467-023-38882-y

Submitted to SASBDB: 2023 Feb 8 Published in SASBDB: 2023 May 5

SASDPK6 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) of SARS-CoV-2 in phosphate conditions Sample: Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein Buffer: 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5 Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Aug 16 RgGuinier 1.6 nm Dmax 6.1 nm VolumePorod 23 nm3

SASDPL6 – 5'-genomic RNA Stem loop 2 and 3 of SARS-CoV-2 in phosphate conditions Sample: Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA Buffer: 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5 Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Nov 22 RgGuinier 2.2 nm Dmax 8.0 nm VolumePorod 24 nm3

SASDPM6 – 5'-genomic RNA Stem loop 4 of SARS-CoV-2 in phosphate conditions Sample: Stem loop 4 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA Buffer: 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5 Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Nov 22 RgGuinier 2.0 nm Dmax 7.1 nm VolumePorod 22 nm3

SASDPN6 – 5'-genomic RNA Stem loop 4 with AU extension of SARS-CoV-2 in phosphate conditions Sample: Stem loop 4 with AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 22 kDa Severe acute respiratory … RNA Buffer: 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5 Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Nov 22 RgGuinier 2.8 nm Dmax 10.2 nm VolumePorod 33 nm3

SASDPP6 – 5'-genomic RNA AU extension of SARS-CoV-2 in phosphate conditions Sample: AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 7 kDa Severe acute respiratory … RNA Buffer: 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5 Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Nov 22 RgGuinier 1.5 nm Dmax 5.4 nm VolumePorod 13 nm3

SASDPQ6 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA Stem loop 2 and 3 of SARS-CoV-2 in phosphate conditions Sample: Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA Buffer: 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5 Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Aug 16 RgGuinier 2.4 nm Dmax 9.0 nm VolumePorod 38 nm3

SASDPR6 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA Stem loop 4 with AU extension of SARS-CoV-2 in phosphate conditions Sample: Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein Stem loop 4 with AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 22 kDa Severe acute respiratory … RNA Buffer: 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5 Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Aug 16 RgGuinier 3.4 nm Dmax 13.5 nm VolumePorod 51 nm3

SASDPS6 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) complexed with 5'-genomic RNA AU extension of SARS-CoV-2 in phosphate conditions Sample: Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 7 kDa Severe acute respiratory … RNA Buffer: 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5 Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Aug 16 RgGuinier 2.1 nm Dmax 8.5 nm VolumePorod 32 nm3

SASDPT6 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) with 5'-genomic RNA Stem loop 4 of SARS-CoV-2 in phosphate conditions (mixture) Sample: Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein Stem loop 4 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA Buffer: 25 mM potassium phosphate, 150 mM KCl, 2 mM TCEP, pH: 6.5 Experiment: SAXS data collected at EMBL P12, PETRA III on 2021 Nov 22 RgGuinier 2.1 nm Dmax 7.8 nm VolumePorod 25 nm3

SASDR33 – N-terminal RNA-binding domain (NTD) of nucleocapsid protein (N) of SARS-CoV-2 in HEPES conditions Sample: Nucleoprotein monomer, 15 kDa Severe acute respiratory … protein Buffer: 25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2 Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29 RgGuinier 1.6 nm Dmax 5.2 nm VolumePorod 26 nm3

SASDR43 – 5'-genomic RNA Stem loop 2 and 3 of SARS-CoV-2 in HEPES conditions Sample: Stem loop 2 and 3 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA Buffer: 25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2 Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29 RgGuinier 2.3 nm Dmax 9.5 nm VolumePorod 28 nm3

SASDR53 – 5'-genomic RNA Stem loop 4 of SARS-CoV-2 in HEPES conditions Sample: Stem loop 4 in the 5'-genomic end of SARS-CoV-2 monomer, 14 kDa Severe acute respiratory … RNA Buffer: 25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2 Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29 RgGuinier 2.1 nm Dmax 7.7 nm VolumePorod 22 nm3

SASDR63 – 5'-genomic RNA Stem loop 4 with AU extension of SARS-CoV-2 in HEPES conditions Sample: Stem loop 4 with AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 22 kDa Severe acute respiratory … RNA Buffer: 25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2 Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29 RgGuinier 3.1 nm Dmax 11.7 nm VolumePorod 35 nm3

SASDR73 – 5'-genomic RNA AU extension of SARS-CoV-2 in HEPES conditions Sample: AU extension in the 5'-genomic end of SARS-CoV-2 monomer, 7 kDa Severe acute respiratory … RNA Buffer: 25 mM HEPES, 75 mM KCl, 2.5 mM NaNO3, pH: 7.2 Experiment: SAXS data collected at EMBL P12, PETRA III on 2022 Nov 29 RgGuinier 1.7 nm Dmax 7.0 nm VolumePorod 13 nm3