9RXL: SARS-CoV-2 nucleocapsid C-terminal domain

SARS-CoV-2 nucleocapsid C-terminal domain in complex with BCY00018176. Determined by X-ray diffraction at 1.46 Å resolution. Released 4 Mar 2026.

Method: X-ray diffraction
Resolution: 1.46 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 4
Atoms: 2,511
Mol. weight: 35.72 kDa
Ligands: LFI
Released: 4 Mar 2026

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

Secondary structure: helices and β-sheets

9RXL contains 24 α-helices and 14 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 and B: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-9	5
α-helix	13-14	2
β-strand	15	1	1

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	2
β-strand	268	1	2
α-helix	270-274	5
β-strand	286	1	3
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	1
β-strand	328-338	11	1
α-helix	346-356	11
β-strand	357	1	3
α-helix	359-362	4

Chain D: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	252-255	4
α-helix	259-261	3
β-strand	265	1	4
β-strand	268	1	4
α-helix	270-274	5
β-strand	286	1	5
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	1
β-strand	328-338	11	1
α-helix	346-356	11
β-strand	357	1	5
α-helix	359-362	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BCY00018176	A, B	protein	18	Homo sapiens
Nucleoprotein	C, D	protein	139	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9RXL_1 BCY00018176 (chains A, B)
ACRVNPCILTGINIPCAX

Sequence of entity 2 (C, D), FASTA

>9RXL_2 Nucleoprotein (chains C, D)
GSTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQI
AQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP
GSSGLNDIFEAQKIEWHEA

Ligands and cofactors

ID	Name	Formula	Copies
LFI	1-[3,5-bis(3-bromanylpropanoyl)-1,3,5-triazinan-1-yl]-3-bromanyl-propan-1-one	C12 H18 Br3 N3 O3	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Utilizing Constrained Bicyclic Peptides for In Vitro Diagnostics. Shamsabadi, A., Creamer, A., Sadler, C.J. et al. ACS Nano (2026) 20:5928-5939. DOI 10.1021/acsnano.5c19041 · 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
9IN1 1.4 Å, Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2
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…

Browse structure collections

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