9IN1: Nucleoprotein

Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2. Determined by X-ray diffraction at 1.4 Å resolution. Released 2 Apr 2025.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 4
Atoms: 4,504
Mol. weight: 53.79 kDa
Released: 2 Apr 2025

Explore 9IN1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IN1 contains 37 α-helices and 24 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B and D: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	259-261	3
β-strand	265	1	1
β-strand	268	1	1
α-helix	270-274	5
β-strand	286	1	2
α-helix	289-294	6
α-helix	295-297	3
α-helix	301-305	5
α-helix	309-310	2
α-helix	311-317	7
β-strand	319-325	7	3
β-strand	328-338	11	3
α-helix	346-356	11
β-strand	357	1	2
α-helix	359-362	4

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	251-254	4
α-helix	259-261	3
β-strand	265	1	6
β-strand	268	1	6
α-helix	270-274	5
β-strand	286	1	7
α-helix	289-294	6
α-helix	295-297	3
α-helix	301-305	5
α-helix	309-310	2
α-helix	311-317	7
β-strand	319-325	7	8
β-strand	328-338	11	8
α-helix	346-356	11
β-strand	357	1	7
α-helix	359-362	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoprotein	A, B, C, D	protein	120	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9IN1_1 Nucleoprotein (chains A, B, C, D)
MGTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQI
AQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP

Primary citation

Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid. Dhaka, P., Mahto, J.K., Singh, A. et al. J Struct Biol (2025) 217:108197-108197. DOI 10.1016/j.jsb.2025.108197 · PubMed

Other PDB entries of the same protein (UniProt P0DTC9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7LUZ 1.1 Å, GQTVTK segment from the Nucleoprotein of SARS-CoV-2, residues 243-248
7LTU 1.12 Å, Aalall segment from the nucleoprotein of SARS-CoV-2, residues 217-222, crystal form 1
7VBF 1.3 Å, 1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization…
9F2H 1.3 Å, Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with riluzole
7LV2 1.3 Å, GSQASS segment from the Nucleoprotein of SARS-CoV-2, residues 179-184
7LUX 1.3 Å, AALALL segment from the Nucleoprotein of SARS-CoV-2, residues 217-222, crystal form 2
7KGQ 1.34 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N222-230
6ZCO 1.36 Å, Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from…
7KGP 1.4 Å, Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N316-324
6WZO 1.42 Å, Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P1 form
7N0R 1.42 Å, Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody…
6YUN 1.44 Å, 1.45 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of…

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