P59595 (NCAP_CVHSA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Nucleoprotein

Alternative name(s):
Nucleocapsid protein
Short name=NC
Short name=Protein N

Gene names

Name:	N
ORF Names:	9a

Organism

Human SARS coronavirus (SARS-CoV) (Severe acute respiratory syndrome coronavirus) [Reference proteome]

Taxonomic identifier

227859 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Nidovirales › Coronaviridae › Coronavirinae › Betacoronavirus › Severe acute respiratory syndrome-related coronavirus

Virus host

Homo sapiens (Human) [TaxID: 9606]
Paguma larvata (Masked palm civet) [TaxID: 9675]

Protein attributes

Sequence length	422 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Major structural component of virions that associates with genomic RNA to form a long, flexible, helical nucleocapsid By similarity.
Subunit structure	Monomer and oligomer. Both monomeric and oligomeric forms interact with RNA. Interacts with the M protein By similarity.
Subcellular location	Virion. Host cytoplasm › host perinuclear region. Host endoplasmic reticulum-Golgi intermediate compartment. Host Golgi apparatus. Note: Located inside the virion, complexed with the viral RNA. Probably associates with ER-derived membranes where it participates in viral RNA synthesis and virus budding. Not found in the nucleolus. Ref.22
Sequence similarities	Belongs to the coronavirus group 2a nucleocapsid protein family.

Ontologies

Keywords
Cellular component	Host Golgi apparatus Host cytoplasm Virion
Ligand	RNA-binding Viral nucleoprotein
Molecular function	Ribonucleoprotein
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Cellular_component	host cell Golgi apparatus Inferred from electronic annotation. Source: UniProtKB-SubCell host cell endoplasmic reticulum-Golgi intermediate compartment Inferred from electronic annotation. Source: UniProtKB-SubCell host cell perinuclear region of cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell ribonucleoprotein complex Inferred from electronic annotation. Source: UniProtKB-KW viral nucleocapsid Non-traceable author statement. Source: UniProtKB
Molecular_function	RNA binding Non-traceable author statement. Source: UniProtKB structural molecule activity Non-traceable author statement. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 422

422

Nucleoprotein

PRO_0000106003

Regions

Region

45 – 181

137

RNA-binding

Region

259 – 367

109

Dimerization By similarity

Compositional bias

181 – 213

33

Ser-rich

Compositional bias

220 – 225

6

Poly-Leu

Compositional bias

240 – 245

6

Poly-Gln

Compositional bias

370 – 376

7

Poly-Lys

Natural variations

Natural variant

50

1

T → I in strain: Isolate Frankfurt 1 and Isolate FRA.

Natural variant

154

1

N → Y in strain: Isolate BJ03.

Natural variant

193

1

G → C in strain: Isolate CUHK-Su10.

Natural variant

325 – 326

2

VT → AA in strain: Isolate Shanghai LY.

Secondary structure

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422

Helix Strand Turn

Details...

Beta strand

56 – 59

4

Beta strand

61 – 63

3

Beta strand

77 – 79

3

Helix

81 – 83

3

Beta strand

85 – 91

7

Beta strand

94 – 96

3

Turn

98 – 100

3

Beta strand

102 – 104

3

Beta strand

108 – 113

6

Turn

118 – 121

4

Beta strand

131 – 135

5

Beta strand

140 – 142

3

Turn

145 – 147

3

Turn

152 – 154

3

Beta strand

254 – 258

5

Helix

260 – 262

3

Helix

271 – 275

5

Turn

282 – 284

3

Helix

290 – 295

6

Helix

296 – 298

3

Helix

302 – 306

5

Helix

312 – 318

7

Beta strand

319 – 325

7

Beta strand

330 – 340

11

Helix

347 – 357

11

Helix

360 – 363

4

Sequences

	Sequence		Length	Mass (Da)
	P59595 [UniParc]. Last modified April 23, 2003. Version 1. Checksum: 43FC8750F1253034	FASTA	422	46,025
	10 20 30 40 50 60 MSDNGPQSNQ RSAPRITFGG PTDSTDNNQN GGRNGARPKQ RRPQGLPNNT ASWFTALTQH 70 80 90 100 110 120 GKEELRFPRG QGVPINTNSG PDDQIGYYRR ATRRVRGGDG KMKELSPRWY FYYLGTGPEA 130 140 150 160 170 180 SLPYGANKEG IVWVATEGAL NTPKDHIGTR NPNNNAATVL QLPQGTTLPK GFYAEGSRGG 190 200 210 220 230 240 SQASSRSSSR SRGNSRNSTP GSSRGNSPAR MASGGGETAL ALLLLDRLNQ LESKVSGKGQ 250 260 270 280 290 300 QQQGQTVTKK SAAEASKKPR QKRTATKQYN VTQAFGRRGP EQTQGNFGDQ DLIRQGTDYK 310 320 330 340 350 360 HWPQIAQFAP SASAFFGMSR IGMEVTPSGT WLTYHGAIKL DDKDPQFKDN VILLNKHIDA 370 380 390 400 410 420 YKTFPPTEPK KDKKKKTDEA QPLPQRQKKQ PTVTLLPAAD MDDFSRQLQN SMSGASADST QA

References

[1]	"Characterization of a novel coronavirus associated with severe acute respiratory syndrome." Rota P.A., Oberste M.S., Monroe S.S., Nix W.A., Campagnoli R., Icenogle J.P., Penaranda S., Bankamp B., Maher K., Chen M.-H., Tong S., Tamin A., Lowe L., Frace M., DeRisi J.L., Chen Q., Wang D., Erdman D.D. , Peret T.C.T., Burns C., Ksiazek T.G., Rollin P.E., Sanchez A., Liffick S., Holloway B., Limor J., McCaustland K., Olsen-Rasmussen M., Fouchier R., Guenther S., Osterhaus A.D.M.E., Drosten C., Pallansch M.A., Anderson L.J., Bellini W.J. Science 300:1394-1399(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate Urbani.
[2]	"The genome sequence of the SARS-associated coronavirus." Marra M.A., Jones S.J.M., Astell C.R., Holt R.A., Brooks-Wilson A., Butterfield Y.S.N., Khattra J., Asano J.K., Barber S.A., Chan S.Y., Cloutier A., Coughlin S.M., Freeman D., Girn N., Griffith O.L., Leach S.R., Mayo M., McDonald H. , Montgomery S.B., Pandoh P.K., Petrescu A.S., Robertson A.G., Schein J.E., Siddiqui A., Smailus D.E., Stott J.M., Yang G.S., Plummer F., Andonov A., Artsob H., Bastien N., Bernard K., Booth T.F., Bowness D., Czub M., Drebot M., Fernando L., Flick R., Garbutt M., Gray M., Grolla A., Jones S., Feldmann H., Meyers A., Kabani A., Li Y., Normand S., Stroher U., Tipples G.A., Tyler S., Vogrig R., Ward D., Watson B., Brunham R.C., Krajden M., Petric M., Skowronski D.M., Upton C., Roper R.L. Science 300:1399-1404(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate Tor2.
[3]	"Coronavirus genomic-sequence variations and the epidemiology of the severe acute respiratory syndrome." Tsui S.K.W., Chim S.S.C., Lo Y.M.D. N. Engl. J. Med. 349:187-188(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate CUHK-Su10 and Isolate CUHK-W1.
[4]	"Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China." Guan Y., Zheng B.J., He Y.Q., Liu X.L., Zhuang Z.X., Cheung C.L., Luo S.W., Li P.H., Zhang L.J., Guan Y.J., Butt K.M., Wong K.L., Chan K.W., Lim W., Shortridge K.F., Yuen K.Y., Peiris J.S.M., Poon L.L.M. Science 302:276-278(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate GZ50 and Isolate HKU-36871.
[5]	"The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39)." Zeng F.Y., Chan C.W., Chan M.N., Chen J.D., Chow K.Y.C., Hon C.C.C., Hui R.K.H., Li J., Li V.Y.Y., Wang C.Y., Wang P.Y., Guan Y., Zheng B., Poon L.L.M., Chan K.H., Yuen K.Y., Peiris J.S.M., Leung F.C. Exp. Biol. Med. 228:866-873(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate HKU-39849.
[6]	"Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection." Ruan Y., Wei C.L., Ling A.E., Vega V.B., Thoreau H., Se Thoe S.Y., Chia J.-M., Ng P., Chiu K.P., Lim L., Zhang T., Chan K.P., Oon L.E.L., Ng M.L., Leo S.Y., Ng L.F.P., Ren E.C., Stanton L.W., Long P.M., Liu E.T. Lancet 361:1779-1785(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate Sin2500, Isolate Sin2677, Isolate Sin2679, Isolate Sin2748 and Isolate sin2774.
[7]	Erratum Ruan Y., Wei C.L., Ling A.E., Vega V.B., Thoreau H., Se Thoe S.Y., Chia J.-M., Ng P., Chiu K.P., Lim L., Zhang T., Chan K.P., Oon L.E.L., Ng M.L., Leo S.Y., Ng L.F.P., Ren E.C., Stanton L.W., Long P.M., Liu E.T. Lancet 361:1832-1832(2003)
[8]	Qin E., Zhu Q., Yu M., Fan B., Chang G., Si B., Yang B., Peng W., Jiang T., Liu B., Deng Y., Liu H., Zhang Y., Wang C., Li Y., Gan Y., Li X., Lu F. , Tan G., Yang R., Cao W.S., Wang J., Chen W., Cong L., Deng Y., Dong W., Han Y., Hu W., Lei M., Li C., Li G., Li G., Li H., Li S., Li S., Li W., Li W., Lin W., Liu J., Liu Z., Lu H., Ni P., Qi Q., Sun Y., Tang L., Tong Z., Wang J., Wang X., Wu Q., Xi Y., Xu Z., Yang L., Ye C., Ye J., Zhang B., Zhang F., Zhang J., Zhang X., Zhou J., Yang H. Submitted (APR-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate BJ01, Isolate BJ02, Isolate BJ03, Isolate BJ04 and Isolate GD01.
[9]	"The complete genome of SARS coronavirus clone TW1." Yeh S.-H., Kao C.-L., Tsai C.-Y., Liu C.-J., Chen D.-S., Chen P.-J. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate TW1.
[10]	"SARS virus is a close relative of type II coronaviruses." Eickmann M., Becker S., Klenk H.-D., Doerr H.W., Stadler K., Censini S., Guidotti S., Masignani V., Scarselli M., Mora M., Donati C., Han J., Song H.C., Abrignani S., Covacci A., Rappuoli R. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate FRA.
[11]	"Mechanisms and enzymes involved in SARS coronavirus genome expression." Thiel V., Ivanov K.A., Putics A., Hertzig T., Schelle B., Bayer S., Weissbrich B., Snijder E.J., Rabenau H., Doerr H.W., Gorbalenya A.E., Ziebuhr J. J. Gen. Virol. 84:2305-2315(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate Frankfurt 1.
[12]	Sun K., Anwar A., Gupta V., Tabiin M.T., Atkinson R., Chandrasekarn A., August T.J. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[13]	"Severe acute respiratory syndrome-associated coronavirus genotype and its characterization." Li L., Wang Z., Lu Y., Bao Q., Chen S., Wu N., Cheng S., Weng J., Zhang Y., Yan J., Mei L., Wang X., Zhu H., Yu Y., Zhang M., Li M., Yao J., Lu Q. , Yao P., Bo X., Wo J., Wang S., Hu S. Chin. Med. J. 116:1288-1292(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate ZJ01.
[14]	"Genomic sequence of SARS isolate from the first fatal case in Taiwan." Yang J.-Y., Lin J.-H., Chiu S.-C., Wang S.-F., Lee S.C., Lin Y.-C., Hsu C.-K., Chen H.-Y., Chang J.G., Chen P.-J., Su I.-J. Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate TWC.
[15]	Yuan Z., Zhang X., Hu Y., Lan S., Wang H., Zhou Z., Wen Y. Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate Shanghai LY.
[16]	Chang J.-G.C., Lin T.-H., Chen C.-M., Lin C.-S., Chan W.-L., Shih M.-C. Submitted (JUL-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate Taiwan TC1, Isolate Taiwan TC2 and Isolate Taiwan TC3.
[17]	"The complete genome of SARS coronavirus TWH." Shu H.Y., Wu K.M., Tsai S.F. Submitted (JUL-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate TWH, Isolate TWJ, Isolate TWK, Isolate TWS and Isolate TWY.
[18]	Canducci F., Clementi M., Poli G., Vicenzi E. Submitted (JUL-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate HSR 1.
[19]	Yang J.-Y., Lin J.-H., Chiu S.-C., Wang S.-F., Lee H.-C., Lin Y.-C., Hsu C.-K., Chen H.-Y., Chen P.-J., Su I.-J. Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate TWC2 and Isolate TWC3.
[20]	Balotta C., Corvasce S., Violin M., Galli M., Moroni M., Vigevani G.M., Ruan Y.J., Salemi M. Submitted (OCT-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate AS.
[21]	"Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein." Saikatendu K.S., Joseph J.S., Subramanian V., Neuman B.W., Buchmeier M.J., Stevens R.C., Kuhn P. J. Virol. 81:3913-3921(2007) [PubMed] [Europe PMC] [Abstract] Cited for: RNA-BINDING. Strain: Isolate Tor2.
[22]	"The intracellular sites of early replication and budding of SARS-coronavirus." Stertz S., Reichelt M., Spiegel M., Kuri T., Martinez-Sobrido L., Garcia-Sastre A., Weber F., Kochs G. Virology 361:304-315(2007) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY278741 Genomic RNA. Translation: AAP13445.1.
AY274119 Genomic RNA. Translation: AAP41047.1.
AY278554 Genomic RNA. Translation: AAP13814.1.
AY282752 Genomic RNA. Translation: AAP30714.1.
AY304492 Genomic RNA. No translation available.
AY304495 Genomic RNA. No translation available.
AY278491 Genomic RNA. No translation available.
AY283794 Genomic RNA. No translation available.
AY283795 Genomic RNA. No translation available.
AY283796 Genomic RNA. No translation available.
AY283797 Genomic RNA. No translation available.
AY278487 Genomic RNA. No translation available.
AY278488 Genomic RNA. Translation: AAP30037.1.
AY278489 Genomic RNA. Translation: AAP51234.1.
AY278490 Genomic RNA. No translation available.
AY279354 Genomic RNA. No translation available.
AY291451 Genomic RNA. Translation: AAP37024.1.
AY310120 Genomic RNA. Translation: AAP50495.1.
AY291315 Genomic RNA. Translation: AAP33707.1.
AY307165 Genomic RNA. Translation: AAP49024.1.
AY290752 Genomic RNA. Translation: AAP44772.1.
AY321118 Genomic RNA. No translation available.
AY322208 Genomic RNA. Translation: AAP82974.1.
AY338174 Genomic RNA. Translation: AAQ01605.1.
AY338175 Genomic RNA. Translation: AAQ01617.1.
AY348314 Genomic RNA. Translation: AAP97890.1.
AP006557 Genomic RNA. Translation: BAC81358.1.
AP006558 Genomic RNA. Translation: BAC81372.1.
AP006559 Genomic RNA. Translation: BAC81386.1.
AP006560 Genomic RNA. Translation: BAC81400.1.
AP006561 Genomic RNA. Translation: BAC81414.1.
AY323977 Genomic RNA. Translation: AAP72984.1.
AY362698 Genomic RNA. No translation available.
AY362699 Genomic RNA. No translation available.
AY427439 Genomic RNA. Translation: AAQ94070.1.

RefSeq

NP_828858.1. NC_004718.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SSK	NMR	-	A	45-181	[»]
1X7Q	X-ray	1.45	C	362-370	[»]
2CJR	X-ray	2.50	A/B/C/D/E/F/G/H	248-365	[»]
2GIB	X-ray	1.75	A/B	270-370	[»]
2JW8	NMR	-	A/B	248-365	[»]
2OFZ	X-ray	1.17	A	49-174	[»]
2OG3	X-ray	1.85	A	49-174	[»]
3I6L	X-ray	2.40	F	346-354	[»]

ProteinModelPortal

P59595.

SMR

P59595. Positions 45-181, 251-365.

ModBase

Search...

Protein-protein interaction databases

MINT

MINT-1346173.

Proteomic databases

PRIDE

P59595.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1489678.

Family and domain databases

InterPro

IPR001218. Corona_nucleocap.
[Graphical view]

Pfam

PF00937. Corona_nucleoca. 1 hit.
[Graphical view]

PIRSF

PIRSF003888. Corona_nucleocap. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P59595.

Entry information

Entry name

NCAP_CVHSA

Accession

Primary (citable) accession number: P59595
Secondary accession number(s): Q7T3Z4 , Q7TA14, Q7TF99, Q80E50

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 23, 2003
Last sequence update:	April 23, 2003
Last modified:	April 3, 2013
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program