7N0R: SARS-CoV-2 N protein RNA-binding domain

Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody C2. Determined by X-ray diffraction at 1.42 Å resolution. Released 2 Jun 2021.

Method: X-ray diffraction
Resolution: 1.42 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Lama glama
Chains: 4
Atoms: 4,574
Mol. weight: 57.55 kDa
Released: 2 Jun 2021

Explore 7N0R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N0R contains 24 α-helices and 42 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.

Chain A: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	1
β-strand	53	1	2
α-helix	54-55	2
β-strand	56-57	2	3
α-helix	63-64	2
α-helix	72-74	3
α-helix	80-82	3
β-strand	84-90	7	3
β-strand	93-95	3	4
β-strand	101-103	3	4
β-strand	107-112	6	3
α-helix	122	1
β-strand	130-134	5	3
β-strand	149	1	1
α-helix	155-156	2
β-strand	157	1	2
α-helix	158-159	2

Chain B: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	5
β-strand	53	1	6
α-helix	54-55	2
β-strand	56-57	2	7
α-helix	63-64	2
α-helix	72-74	3
α-helix	80-82	3
β-strand	84-90	7	7
β-strand	93-95	3	8
β-strand	101-103	3	8
β-strand	107-112	6	7
α-helix	116-118	3
α-helix	122	1
β-strand	130-134	5	7
β-strand	149	1	5
α-helix	155-156	2
β-strand	157	1	6
α-helix	158	1

Chain C: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-39	6	11
β-strand	46-51	6	11
β-strand	58-60	3	11
β-strand	68-73	6	9
α-helix	74-76	3
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	11
α-helix	109-111	3
β-strand	115-117	3	11
β-strand	118-119	2	10

Chain D: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	11-12	2	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	14
α-helix	44-45	2
β-strand	46-51	6	14
β-strand	58-60	3	14
β-strand	68-73	6	12
α-helix	74-76	3
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-98	7	14
α-helix	109-111	3
β-strand	115-117	3	14
β-strand	118-119	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoprotein	A, B	protein	129	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)
Single-domain antibody C2	C, D	protein	134	Lama glama

Sequence of entity 1 (A, B), FASTA

>7N0R_1 Nucleoprotein (chains A, B)
SNATASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLS
PRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGT
TLPKGFYAE

Sequence of entity 2 (C, D), FASTA

>7N0R_2 Single-domain antibody C2 (chains C, D)
MAEVQLQASGGGLVRPGGSLRLSCAASGFTFSSYAMMWVRQAPGKGLEWVSAINGGGGST
SYADSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAKYQAAVHQEKEDYWGQGTQVT
VSSAAALEHHHHHH

Primary citation

Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies. Ye, Q., Lu, S., Corbett, K.D. Front Immunol (2021) 12:719037-719037. DOI 10.3389/fimmu.2021.719037 · 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
6YUN 1.44 Å, 1.45 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of…

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