6VYO: Nucleoprotein

Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2. Determined by X-ray diffraction at 1.7 Å resolution. Released 11 Mar 2020.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 4
Atoms: 4,683
Mol. weight: 57.67 kDa
Ligands: ZN
Released: 11 Mar 2020

Explore 6VYO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VYO contains 34 α-helices and 41 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	53	1	1
α-helix	54-55	2
β-strand	56-57	2	2
α-helix	63-64	2
α-helix	72-74	3
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	93-95	3	3
β-strand	101-103	3	3
α-helix	104-106	3
β-strand	107-112	6	2
α-helix	122	1
β-strand	130-134	5	2
α-helix	155-156	2
β-strand	157	1	1
α-helix	158-159	2

Chain B: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	4
β-strand	53	1	5
α-helix	54-55	2
β-strand	56-58	3	6
α-helix	63-64	2
α-helix	72-74	3
α-helix	80-82	3
β-strand	84-90	7	6
β-strand	93-95	3	7
β-strand	101-103	3	7
α-helix	104-106	3
β-strand	107-112	6	6
α-helix	121-122	2
β-strand	130-134	5	6
β-strand	149	1	4
α-helix	155-156	2
β-strand	157	1	5
α-helix	158-159	2
α-helix	167-168	2
β-strand	171-172	2	6

Chain C: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	8
β-strand	53	1	9
α-helix	54-55	2
β-strand	56-57	2	10
α-helix	63-64	2
α-helix	72-74	3
α-helix	80-82	3
β-strand	84-90	7	10
β-strand	93-95	3	11
β-strand	101-103	3	11
α-helix	104-106	3
β-strand	107-112	6	10
α-helix	122	1
β-strand	127	1	10
β-strand	130-134	5	10
β-strand	149	1	8
α-helix	155-156	2
β-strand	157	1	9
α-helix	158-159	2

Chain D: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	12
β-strand	53	1	13
α-helix	54-55	2
β-strand	56-58	3	14
α-helix	63-64	2
α-helix	72-74	3
α-helix	80-82	3
β-strand	84-90	7	14
β-strand	93-95	3	15
β-strand	101-103	3	15
α-helix	104-106	3
β-strand	107-112	6	14
α-helix	122	1
β-strand	130-134	5	14
β-strand	149	1	12
α-helix	155-156	2
β-strand	157	1	13
α-helix	158-159	2
α-helix	167-168	2
β-strand	171-172	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoprotein	A, B, C, D	protein	128	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)

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

>6VYO_1 Nucleoprotein (chains A, B, C, D)
GNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLS
PRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGT
TLPKGFYA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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

Primary citation

Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. Kim, Y., Maltseva, N., Tesar, C. et al. iScience (2024) 27:108976-108976. DOI 10.1016/j.isci.2024.108976 · 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…

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6VYO is part of these collections:

SARS-CoV-2 and COVID-19

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