Dynamic ensembles of SARS-CoV-2 N-protein reveal head-to-head coiled-coil-driven oligomerization and phase separation.

Hernandez G, Martins ML, Fernandes NP, Veloso T, Lopes J, Gomes T, Cordeiro TN
Nucleic Acids Res 53(11) (2025 Jun 6)

PMID: 40503686 doi: 10.1093/nar/gkaf502

Submitted to SASBDB: 2023 Sep 21 Published in SASBDB: 2025 Feb 10

SASDTE5 – SARS-CoV-2 N-protein (N1-365, amino acids 1-365): 26 µM Sample: Nucleoprotein dimer, 82 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 5.7 nm Dmax 23.0 nm VolumePorod 160 nm3

SASDTF5 – SARS-CoV-2 N-protein (N1-365, amino acids 1-365): 49 µM Sample: Nucleoprotein tetramer, 163 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 5.8 nm Dmax 24.0 nm VolumePorod 181 nm3

SASDTG5 – SARS-CoV-2 N-protein (N1-365, amino acids 1-365): 103 µM Sample: Nucleoprotein tetramer, 163 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 6.2 nm Dmax 25.0 nm VolumePorod 215 nm3

SASDTH5 – SARS-CoV-2 N-protein (N1-365, amino acids 1-365): 206 µM Sample: Nucleoprotein tetramer, 163 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 6.8 nm Dmax 28.0 nm VolumePorod 578 nm3

SASDTJ5 – SARS-CoV-2 N-protein (N1-365, amino acids 1-365): 299 µM Sample: Nucleoprotein hexamer, 245 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 7.1 nm Dmax 29.0 nm VolumePorod 708 nm3

SASDTX5 – SARS-CoV-2 N-protein Full Length (N1-419, amino acids 1-419): 19 µM Sample: Nucleoprotein tetramer, 187 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 6.3 nm Dmax 26.0 nm VolumePorod 233 nm3

SASDTY5 – SARS-CoV-2 N-protein Full Length (N1-419, amino acids 1-419): 50 µM Sample: Nucleoprotein tetramer, 187 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 6.9 nm Dmax 28.5 nm VolumePorod 571 nm3

SASDTZ5 – SARS-CoV-2 N-protein Full Length (N1-419, amino acids 1-419): 103 µM Sample: Nucleoprotein hexamer, 281 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 7.6 nm Dmax 32.0 nm VolumePorod 764 nm3

SASDT26 – SARS-CoV-2 N-protein Full Length (N1-419, amino acids 1-419): 216 µM Sample: Nucleoprotein octamer, 375 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 8.2 nm Dmax 33.0 nm VolumePorod 1028 nm3

SASDSZ9 – SARS-CoV-2 N-protein InterDomain Linker (IDL, residues 176-245): 238 µM Sample: Nucleoprotein monomer, 8 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at BM29, ESRF on 2023 Jan 29 RgGuinier 3.2 nm Dmax 14.0 nm VolumePorod 19 nm3

SASDT22 – SARS-CoV-2 N-protein InterDomain Linker (IDL, residues 176-245): 476 µM Sample: Nucleoprotein monomer, 8 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at BM29, ESRF on 2023 Jan 29 RgGuinier 3.7 nm Dmax 16.0 nm VolumePorod 33 nm3

SASDT32 – SARS-CoV-2 N-protein InterDomain Linker (IDL, residues 176-245): 952 µM Sample: Nucleoprotein dimer, 17 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at BM29, ESRF on 2023 Jan 29 RgGuinier 4.1 nm Dmax 18.0 nm VolumePorod 53 nm3

SASDVS6 – SARS-CoV-2 N-protein InterDomain Linker (IDL, amino acids 176-245): 1666.7 µM Sample: Nucleoprotein dimer, 17 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at BM29, ESRF on 2023 Jan 29 RgGuinier 4.5 nm Dmax 19.0 nm VolumePorod 117 nm3

SASDT42 – SARS-CoV-2 N-protein InterDomain Linker (IDL, residues 176-245) L223P, L227P and L230P triple mutant: 238 µM Sample: Nucleoprotein (L223P, L227P, L230P) monomer, 8 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at BM29, ESRF on 2023 Jan 29 RgGuinier 2.4 nm Dmax 11.0 nm VolumePorod 10 nm3

SASDT52 – SARS-CoV-2 N-protein InterDomain Linker (IDL, residues 176-245) L223P, L227P and L230P triple mutant: 476 µM Sample: Nucleoprotein (L223P, L227P, L230P) monomer, 8 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at BM29, ESRF on 2023 Jan 29 RgGuinier 2.7 nm Dmax 11.0 nm VolumePorod 12 nm3

SASDT62 – SARS-CoV-2 N-protein InterDomain Linker (IDL, residues 176-245) L223P, L227P and L230P triple mutant: 952 µM Sample: Nucleoprotein (L223P, L227P, L230P) monomer, 8 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at BM29, ESRF on 2023 Jan 29 RgGuinier 2.7 nm Dmax 12.0 nm VolumePorod 13 nm3

SASDVT6 – SARS-CoV-2 N-protein InterDomain Linker (IDL, amino acids 176-245) L223P, L227P and L230P triple mutant: 1667 µM Sample: Nucleoprotein (L223P, L227P, L230P) monomer, 8 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at BM29, ESRF on 2023 Jan 29 RgGuinier 2.8 nm Dmax 12.0 nm VolumePorod 14 nm3

SASDST9 – SARS-CoV-2 N-protein (N1-245; residues 1-245): 294.7 µM Sample: Nucleoprotein tetramer, 110 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 5.2 nm Dmax 22.0 nm VolumePorod 117 nm3

SASDSR9 – SARS-CoV-2 N-protein (N1-245; residues 1-245): 38.2 µM Sample: Nucleoprotein monomer, 27 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 3.3 nm Dmax 15.5 nm VolumePorod 56 nm3

SASDSS9 – SARS-CoV-2 N-protein (N1-245, residues 1-245): 76.4 µM Sample: Nucleoprotein dimer, 55 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 4.0 nm Dmax 18.0 nm VolumePorod 67 nm3

SASDSU9 – SARS-CoV-2 N-protein (N1-245, residues 1-245): 400 µM Sample: Nucleoprotein tetramer, 110 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 5.4 nm Dmax 24.0 nm VolumePorod 157 nm3

SASDSV9 – SARS-CoV-2 N-protein (N1-245; residues 1-245) L223P, L227P and L230P triple mutant: 36.4 µM Sample: Nucleoprotein (L223P, L227P, L230P) monomer, 27 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Jan 29 RgGuinier 3.2 nm Dmax 13.5 nm VolumePorod 53 nm3

SASDSW9 – SARS-CoV-2 N-protein (N1-245, residues 1-245) L223P, L227P and L230P triple mutant: 72.7 µM Sample: Nucleoprotein (L223P, L227P, L230P) monomer, 27 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Jan 29 RgGuinier 3.5 nm Dmax 14.5 nm VolumePorod 47 nm3

SASDVU6 – SARS-CoV-2 N-protein (N1-245; amino acids 1-245): 167 µM Sample: Nucleoprotein dimer, 55 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2022 May 13 RgGuinier 5.2 nm Dmax 20.5 nm VolumePorod 121 nm3

SASDSX9 – SARS-CoV-2 N-protein (N1-245, residues 1-245) L223P, L227P and L230P triple mutant: 294 µM Sample: Nucleoprotein (L223P, L227P, L230P) monomer, 27 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Jan 29 RgGuinier 4.4 nm Dmax 19.0 nm VolumePorod 68 nm3

SASDSY9 – SARS-CoV-2 N-protein (N1-245, residues 1-245) L223P, L227P and L230P triple mutant: 400 µM Sample: Nucleoprotein (L223P, L227P, L230P) monomer, 27 kDa Severe acute respiratory … protein Buffer: 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH: 8 Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Jan 29 RgGuinier 4.6 nm Dmax 19.0 nm VolumePorod 75 nm3