2CJR: Nucleocapsid protein

Crystal structure of oligomerization domain of SARS coronavirus nucleocapsid protein. Determined by X-ray diffraction at 2.5 Å resolution. Released 10 Apr 2007.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: SARS CORONAVIRUS
Chains: 8
Atoms: 7,973
Mol. weight: 116.48 kDa
Released: 10 Apr 2007

Explore 2CJR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2CJR contains 71 α-helices and 40 β-strands across 8 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
β-strand	266	1	1
β-strand	269	1	1
α-helix	271-275	5
β-strand	287	1	2
α-helix	290-295	6
α-helix	296-298	3
α-helix	302-306	5
α-helix	310-311	2
α-helix	312-317	6
β-strand	322-325	4	3
β-strand	330-339	10	3
α-helix	347-357	11
β-strand	358	1	2
α-helix	360-362	3

Chain B: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
β-strand	266	1	4
β-strand	269	1	4
α-helix	271-275	5
α-helix	290-295	6
α-helix	296-298	3
α-helix	302-306	5
α-helix	312-318	7
β-strand	320-326	7	3
β-strand	329-339	11	3
α-helix	347-357	11
α-helix	360-363	4

Chain C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
β-strand	266	1	5
β-strand	269	1	5
α-helix	271-275	5
β-strand	287	1	6
α-helix	290-295	6
α-helix	296-298	3
α-helix	302-306	5
α-helix	312-318	7
β-strand	320-325	6	7
β-strand	330-340	11	7
α-helix	347-357	11
β-strand	358	1	6
α-helix	360-363	4

Chain D: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
α-helix	271-275	5
α-helix	290-295	6
α-helix	296-298	3
α-helix	302-306	5
α-helix	310-311	2
α-helix	312-318	7
β-strand	320-326	7	7
β-strand	329-339	11	7
α-helix	340	1
α-helix	347-357	11
α-helix	360-363	4

Chain E: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
α-helix	271-275	5
β-strand	278	1	8
β-strand	285	1	8
α-helix	290-295	6
α-helix	296-298	3
α-helix	302-306	5
α-helix	310-311	2
α-helix	313-316	4
β-strand	320-323	4	9
β-strand	326	1	10
β-strand	329	1	10
β-strand	331-339	9	9
α-helix	347-357	11
α-helix	360-362	3

Chain F: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
α-helix	263-265	3
α-helix	271-275	5
β-strand	287	1	11
α-helix	290-295	6
α-helix	296-298	3
α-helix	302-305	4
α-helix	306-308	3
α-helix	310-311	2
α-helix	312-318	7
β-strand	320-324	5	9
β-strand	331-339	9	9
α-helix	349-357	9
β-strand	358	1	11

Chain G: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
α-helix	271-275	5
β-strand	278	1	12
β-strand	285	1	12
α-helix	290-295	6
α-helix	296-298	3
α-helix	302-306	5
α-helix	310-311	2
α-helix	312-318	7
β-strand	320-325	6	13
β-strand	330-339	10	13
α-helix	345-347	3
α-helix	349-358	10

Chain H: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	260-262	3
β-strand	266	1	14
β-strand	269	1	14
α-helix	271-275	5
β-strand	278	1	15
β-strand	285	1	15
β-strand	287	1	16
α-helix	290-295	6
α-helix	296-298	3
α-helix	302-306	5
α-helix	310-311	2
α-helix	312-318	7
β-strand	320-324	5	13
β-strand	331-339	9	13
α-helix	347-357	11
β-strand	358	1	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleocapsid protein	A, B, C, D, E, F, G, H	protein	128	SARS CORONAVIRUS	P59595 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>2CJR_1 NUCLEOCAPSID PROTEIN (chains A, B, C, D, E, F, G, H)
MHHHHHHAMGTKKSAAEASKKPRQKRTATKQYNVTQAFGRRGPEQTQGNFGDQDLIRQGT
DYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYHGAIKLDDKDPQFKDNVILLNKH
IDAYKTFP

Primary citation

Structure of the Sars Coronavirus Nucleocapsid Protein RNA-Binding Dimerization Domain Suggests a Mechanism for Helical Packaging of Viral RNA. Chen, C.-Y., Chang, C.K., Chang, Y.W. et al. J Mol Biol (2007) 368:1075. DOI 10.1016/J.JMB.2007.02.069 · PubMed

Other PDB entries of the same protein (UniProt P59595 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OFZ 1.17 Å, Ultrahigh Resolution Crystal Structure of RNA Binding Domain of SARS Nucleopcapsid (N…
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide
2GIB 1.75 Å, Crystal structure of the SARS coronavirus nucleocapsid protein dimerization domain
2OG3 1.85 Å, structure of the rna binding domain of n protein from SARS coronavirus in cubic crystal…
7LG0 2.3 Å, Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope SPRWYFYYL
6IEX 2.31 Å, Crystal structure of HLA-B*4001 in complex with SARS-CoV derived peptide N216-225…
3I6L 2.4 Å, Newly identified epitope N1 derived from SARS-CoV N protein complexed with HLA-A*2402
1SSK Structure of the N-terminal RNA-binding Domain of the SARS CoV Nucleocapsid Protein
2JW8 Solution structure of stereo-array isotope labelled (SAIL) C-terminal dimerization…

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