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Protein

Spike glycoprotein

Gene

S

Organism
Human SARS coronavirus (SARS-CoV) (Severe acute respiratory syndrome coronavirus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

S1 attaches the virion to the cell membrane by interacting with human ACE2 and CLEC4M/DC-SIGNR, initiating the infection. Binding to the receptor and internalization of the virus into the endosomes of the host cell probably induces conformational changes in the S glycoprotein. Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.
S2 is a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.

GO - Molecular functioni

  • host cell surface receptor binding Source: BHF-UCL

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Fusion of virus membrane with host endosomal membrane, Fusion of virus membrane with host membrane, Host-virus interaction, Viral attachment to host cell, Viral penetration into host cytoplasm, Virulence, Virus entry into host cell

Names & Taxonomyi

Protein namesi
Recommended name:
Spike glycoprotein
Short name:
S glycoprotein
Alternative name(s):
E2
Peplomer protein
Cleaved into the following 2 chains:
Gene namesi
Name:S
ORF Names:2
OrganismiHuman SARS coronavirus (SARS-CoV) (Severe acute respiratory syndrome coronavirus)
Taxonomic identifieri227859 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageNidoviralesCoronaviridaeCoronavirinaeBetacoronavirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Paguma larvata (Masked palm civet) [TaxID: 9675]
Proteomesi
  • UP000000354 Componenti: Genome

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini14 – 11951182ExtracellularSequence analysisAdd
BLAST
Transmembranei1196 – 121621HelicalSequence analysisAdd
BLAST
Topological domaini1217 – 125539CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Host cell membrane, Host membrane, Membrane, Viral envelope protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi323 – 3231C → A: No effect on human ACE2 binding in vitro. 1 Publication
Mutagenesisi348 – 3481C → A: Complete loss of human ACE2 binding in vitro. 1 Publication
Mutagenesisi452 – 4521E → A: 90% loss of human ACE2 binding in vitro. 1 Publication
Mutagenesisi454 – 4541D → A: Complete loss of human ACE2 binding in vitro. 1 Publication
Mutagenesisi463 – 4631D → A: Partial loss of human ACE2 binding in vitro. 1 Publication
Mutagenesisi467 – 4671C → A: Complete loss of human ACE2 binding in vitro. 1 Publication
Mutagenesisi474 – 4741C → A: Complete loss of human ACE2 binding in vitro. 1 Publication
Mutagenesisi480 – 4801D → A: No effect on human ACE2 binding in vitro. 1 Publication
Mutagenesisi667 – 6671R → S: 40% loss of cell-cell fusion. 1 Publication
Mutagenesisi672 – 6721K → S: No effect on cell-cell fusion. 1 Publication
Mutagenesisi1251 – 12511K → A: Decrease in Golgi localization, and complete loss of COPI binding; when associated to A-1253. 1 Publication
Mutagenesisi1253 – 12531H → A: Decrease in Golgi localization, and complete loss of COPI binding; when associated to A-1251. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1313Sequence analysisAdd
BLAST
Chaini14 – 12551242Spike glycoproteinPRO_0000037208Add
BLAST
Chaini14 – 667654Spike protein S1Sequence analysisPRO_0000037209Add
BLAST
Chaini668 – 1255588Spike protein S2Sequence analysisPRO_0000037210Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi29 – 291N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi65 – 651N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi73 – 731N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi109 – 1091N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi118 – 1181N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi119 – 1191N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi158 – 1581N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi227 – 2271N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi269 – 2691N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi318 – 3181N-linked (GlcNAc...); by hostSequence analysis
Disulfide bondi323 ↔ 348
Glycosylationi330 – 3301N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi357 – 3571N-linked (GlcNAc...); by hostSequence analysis
Disulfide bondi366 ↔ 419
Disulfide bondi467 ↔ 474
Glycosylationi589 – 5891N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi602 – 6021N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi691 – 6911N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi699 – 6991N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi783 – 7831N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi1056 – 10561N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi1080 – 10801N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi1116 – 11161N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi1140 – 11401N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi1155 – 11551N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi1176 – 11761N-linked (GlcNAc...); by hostSequence analysis

Post-translational modificationi

The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested by cathepsin CTSL within endosomes.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei667 – 6682CleavageSequence analysis

Keywords - PTMi

Disulfide bond, Glycoprotein, Lipoprotein, Palmitate

Interactioni

Subunit structurei

Homotrimer. Binds to human and palm civet ACE2 and human CLEC4M/DC-SIGNR. Interacts with the accessory proteins 3a and 7a.6 Publications

GO - Molecular functioni

  • host cell surface receptor binding Source: BHF-UCL

Protein-protein interaction databases

DIPiDIP-29105N.

Structurei

Secondary structure

1
1255
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi326 – 3294Combined sources
Helixi337 – 3393Combined sources
Beta strandi341 – 3455Combined sources
Beta strandi347 – 3493Combined sources
Helixi352 – 3543Combined sources
Beta strandi362 – 3687Combined sources
Helixi371 – 3788Combined sources
Beta strandi380 – 39011Combined sources
Helixi391 – 3966Combined sources
Beta strandi397 – 4004Combined sources
Helixi404 – 4085Combined sources
Beta strandi418 – 4247Combined sources
Helixi426 – 4294Combined sources
Beta strandi431 – 4333Combined sources
Beta strandi439 – 4413Combined sources
Beta strandi462 – 4643Combined sources
Beta strandi469 – 4713Combined sources
Beta strandi478 – 4803Combined sources
Beta strandi483 – 4875Combined sources
Helixi489 – 4913Combined sources
Beta strandi492 – 50110Combined sources
Beta strandi509 – 5113Combined sources
Helixi773 – 7775Combined sources
Helixi780 – 7834Combined sources
Turni784 – 7863Combined sources
Helixi879 – 8879Combined sources
Beta strandi898 – 9003Combined sources
Helixi915 – 94834Combined sources
Helixi1148 – 11514Combined sources
Helixi1162 – 117211Combined sources
Helixi1173 – 11786Combined sources
Helixi1182 – 119211Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Q4Zmodel-A17-680[»]
1T7Gmodel-A/C/E17-680[»]
B/D/F737-1026[»]
1U4Kmodel-D764-1089[»]
1WNCX-ray2.80A/B/C/D/E/F900-948[»]
A/B/C/D/E/F1144-1185[»]
1WYYX-ray2.20A/B885-981[»]
A/B1145-1189[»]
1XJPmodel-A17-680[»]
1ZV7X-ray1.70A/B1150-1193[»]
1ZV8X-ray1.94A/C/E/G/I/K901-950[»]
B/D/F/H/J/L1150-1185[»]
1ZVBX-ray1.70A/B/C940-973[»]
2AJFX-ray2.90E/F323-502[»]
2BEQX-ray1.60A/B/C914-949[»]
D/E/F1148-1193[»]
2BEZX-ray1.60C896-972[»]
F1142-1183[»]
2DD8X-ray2.30S317-518[»]
2FXPNMR-A/B/C1141-1193[»]
2GHVX-ray2.20C/E317-510[»]
2GHWX-ray2.30A/C317-510[»]
2RUMNMR-A770-788[»]
2RUNNMR-A1185-1202[»]
2RUONMR-A873-888[»]
3BGFX-ray3.00A/S318-510[»]
3D0GX-ray2.80E/F324-502[»]
3D0HX-ray3.10E/F324-502[»]
3D0IX-ray2.90E/F324-502[»]
3SCIX-ray2.90E/F306-527[»]
3SCJX-ray3.00E/F323-502[»]
3SCKX-ray3.00E/F324-502[»]
3SCLX-ray3.00E/F324-502[»]
ProteinModelPortaliP59594.
SMRiP59594. Positions 321-512, 896-972, 1148-1193.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP59594.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni306 – 527222Receptor-binding domainAdd
BLAST
Regioni424 – 49471Receptor-binding motif; binding to human ACE2Add
BLAST
Regioni770 – 78819Fusion peptideSequence analysisAdd
BLAST
Regioni902 – 95251Heptad repeat 1Add
BLAST
Regioni1145 – 118440Heptad repeat 2Add
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili931 – 97545Sequence analysisAdd
BLAST
Coiled coili1157 – 118529Sequence analysisAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1251 – 12555KxHxx

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi1217 – 123620Cys-richAdd
BLAST

Domaini

The KxHxx motif seems to function as an ER retrieval and binds COPI in vitro.

Sequence similaritiesi

Belongs to the coronaviruses spike protein family.Curated

Keywords - Domaini

Coiled coil, Signal, Transmembrane, Transmembrane helix

Family and domain databases

Gene3Di1.20.5.790. 1 hit.
InterProiIPR002552. Corona_S2.
IPR027400. S_HR2.
IPR032500. Spike_N.
IPR018548. Spike_rcpt-bd.
[Graphical view]
PfamiPF01601. Corona_S2. 1 hit.
PF16451. Spike_NTD. 1 hit.
PF09408. Spike_rec_bind. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P59594-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFIFLLFLTL TSGSDLDRCT TFDDVQAPNY TQHTSSMRGV YYPDEIFRSD
60 70 80 90 100
TLYLTQDLFL PFYSNVTGFH TINHTFGNPV IPFKDGIYFA ATEKSNVVRG
110 120 130 140 150
WVFGSTMNNK SQSVIIINNS TNVVIRACNF ELCDNPFFAV SKPMGTQTHT
160 170 180 190 200
MIFDNAFNCT FEYISDAFSL DVSEKSGNFK HLREFVFKNK DGFLYVYKGY
210 220 230 240 250
QPIDVVRDLP SGFNTLKPIF KLPLGINITN FRAILTAFSP AQDIWGTSAA
260 270 280 290 300
AYFVGYLKPT TFMLKYDENG TITDAVDCSQ NPLAELKCSV KSFEIDKGIY
310 320 330 340 350
QTSNFRVVPS GDVVRFPNIT NLCPFGEVFN ATKFPSVYAW ERKKISNCVA
360 370 380 390 400
DYSVLYNSTF FSTFKCYGVS ATKLNDLCFS NVYADSFVVK GDDVRQIAPG
410 420 430 440 450
QTGVIADYNY KLPDDFMGCV LAWNTRNIDA TSTGNYNYKY RYLRHGKLRP
460 470 480 490 500
FERDISNVPF SPDGKPCTPP ALNCYWPLND YGFYTTTGIG YQPYRVVVLS
510 520 530 540 550
FELLNAPATV CGPKLSTDLI KNQCVNFNFN GLTGTGVLTP SSKRFQPFQQ
560 570 580 590 600
FGRDVSDFTD SVRDPKTSEI LDISPCSFGG VSVITPGTNA SSEVAVLYQD
610 620 630 640 650
VNCTDVSTAI HADQLTPAWR IYSTGNNVFQ TQAGCLIGAE HVDTSYECDI
660 670 680 690 700
PIGAGICASY HTVSLLRSTS QKSIVAYTMS LGADSSIAYS NNTIAIPTNF
710 720 730 740 750
SISITTEVMP VSMAKTSVDC NMYICGDSTE CANLLLQYGS FCTQLNRALS
760 770 780 790 800
GIAAEQDRNT REVFAQVKQM YKTPTLKYFG GFNFSQILPD PLKPTKRSFI
810 820 830 840 850
EDLLFNKVTL ADAGFMKQYG ECLGDINARD LICAQKFNGL TVLPPLLTDD
860 870 880 890 900
MIAAYTAALV SGTATAGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLYE
910 920 930 940 950
NQKQIANQFN KAISQIQESL TTTSTALGKL QDVVNQNAQA LNTLVKQLSS
960 970 980 990 1000
NFGAISSVLN DILSRLDKVE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI
1010 1020 1030 1040 1050
RASANLAATK MSECVLGQSK RVDFCGKGYH LMSFPQAAPH GVVFLHVTYV
1060 1070 1080 1090 1100
PSQERNFTTA PAICHEGKAY FPREGVFVFN GTSWFITQRN FFSPQIITTD
1110 1120 1130 1140 1150
NTFVSGNCDV VIGIINNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD
1160 1170 1180 1190 1200
ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ YIKWPWYVWL
1210 1220 1230 1240 1250
GFIAGLIAIV MVTILLCCMT SCCSCLKGAC SCGSCCKFDE DDSEPVLKGV

KLHYT
Length:1,255
Mass (Da):139,125
Last modified:April 23, 2003 - v1
Checksum:i1C49ACA2CFD38FC0
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti49 – 491S → L in strain: Isolate GZ50.
Natural varianti77 – 771G → D in strain: Isolate BJ01, Isolate BJ02, Isolate BJ03, Isolate GZ50, Isolate CUHK-W1, Isolate HKU-36871, Isolate GD01, Isolate GD03 and Isolate SZ3.
Natural varianti78 – 781N → D in strain: Isolate GD03.
Natural varianti118 – 1181N → S in strain: Isolate Shanghai LY.
Natural varianti139 – 1391A → V in strain: Isolate GD03.
Natural varianti144 – 1441M → L in strain: Isolate BJ03.
Natural varianti147 – 1471Q → R in strain: Isolate GD03.
Natural varianti193 – 1931F → S in strain: Isolate Shanghai LY.
Natural varianti227 – 2271N → K in strain: Isolate SZ3.
Natural varianti239 – 2391S → L in strain: Isolate GD01 and Isolate SZ3.
Natural varianti244 – 2441I → T in strain: Isolate BJ01, Isolate BJ02, Isolate BJ03, Isolate BJ04, Isolate GZ50, Isolate CUHK-W1, Isolate HKU-36871, Isolate GD01, Isolate GD03 and Isolate SZ3.
Natural varianti261 – 2611T → K in strain: Isolate SZ3.
Natural varianti311 – 3111G → R in strain: Isolate GD01 and Isolate BJ02.
Natural varianti344 – 3441K → R in strain: Isolate GD01, Isolate GD03 and Isolate SZ3; no effect on affinity with either human or palm civet ACE2. 1 Publication
Natural varianti360 – 3601F → S in strain: Isolate GD03 and Isolate SZ3; no effect on affinity with either human or palm civet ACE2. 1 Publication
Natural varianti426 – 4261R → G in strain: Isolate Shanghai LY.
Natural varianti437 – 4371N → D in strain: Isolate Shanghai LY.
Natural varianti472 – 4721L → P in strain: Isolate GD03.
Natural varianti479 – 4791N → K in strain: Isolate SZ3; 20fold decrease of affinity with human ACE2; no effect on affinity with palm civet ACE2. 1 Publication
Natural varianti480 – 4801D → G in strain: Isolate GD03.
Natural varianti487 – 4871T → S in strain: Isolate GD03 and Isolate SZ3; 20fold decrease of affinity with human ACE2; decrease of affinity with palm civet ACE2. 1 Publication
Natural varianti501 – 5011F → Y in strain: Isolate GD01.
Natural varianti577 – 5771S → A in strain: Isolate Tor2 and Isolate Shanghai QXC1.
Natural varianti605 – 6051D → N in strain: Isolate Shanghai QXC1.
Natural varianti607 – 6071S → P in strain: Isolate SZ3.
Natural varianti608 – 6081T → A in strain: Isolate Shanghai QXC1.
Natural varianti609 – 6091A → L in strain: Isolate GD03.
Natural varianti613 – 6131D → E in strain: Isolate GD03.
Natural varianti665 – 6651L → S in strain: Isolate GD03 and Isolate SZ3.
Natural varianti701 – 7011S → L in strain: Isolate SZ3.
Natural varianti743 – 7431T → A in strain: Isolate SZ3.
Natural varianti743 – 7431T → R in strain: Isolate GD03.
Natural varianti754 – 7541A → V in strain: Isolate SZ3.
Natural varianti765 – 7651A → V in strain: Isolate GD03.
Natural varianti778 – 7781Y → D in strain: Isolate GD01, Isolate GZ50, Isolate GD03 and Isolate SZ3.
Natural varianti794 – 7941P → S in strain: Isolate GD01.
Natural varianti804 – 8041L → P in strain: Isolate Shanghai LY.
Natural varianti860 – 8612VS → LR in strain: Isolate BJ03.
Natural varianti894 – 8941T → A in strain: Isolate SZ3.
Natural varianti999 – 9991E → G in strain: Isolate Shanghai LY.
Natural varianti1001 – 10011R → M in strain: Isolate BJ04.
Natural varianti1132 – 11321E → G in strain: Isolate Shanghai QXC1.
Natural varianti1148 – 11481L → F in strain: Isolate Frankfurt 1 and Isolate FRA.
Natural varianti1163 – 11631K → E in strain: Isolate GD03 and Isolate SZ3.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY278741 Genomic RNA. Translation: AAP13441.1.
AY274119 Genomic RNA. Translation: AAP41037.1.
AY282752 Genomic RNA. Translation: AAP30713.1.
AY278554 Genomic RNA. Translation: AAP13567.1.
AY278491 Genomic RNA. No translation available.
AY304495 Genomic RNA. No translation available.
AY304492 Genomic RNA. No translation available.
AY278487 Genomic RNA. No translation available.
AY278488 Genomic RNA. Translation: AAP30030.1.
AY278490 Genomic RNA. No translation available.
AY279354 Genomic RNA. No translation available.
AY278489 Genomic RNA. Translation: AAP51227.1.
AY283794 Genomic RNA. No translation available.
AY283795 Genomic RNA. No translation available.
AY283796 Genomic RNA. No translation available.
AY283797 Genomic RNA. No translation available.
AY283798 Genomic RNA. No translation available.
AY291451 Genomic RNA. Translation: AAP37017.1.
AY310120 Genomic RNA. Translation: AAP50485.1.
AY291315 Genomic RNA. Translation: AAP33697.1.
AY304486 Genomic RNA. No translation available.
AY321118 Genomic RNA. No translation available.
AY323976 mRNA. Translation: AAP73417.1.
AY322207 Genomic RNA. Translation: AAP82968.1.
AY338174 Genomic RNA. Translation: AAQ01597.1.
AY338175 Genomic RNA. Translation: AAQ01609.1.
AY348314 Genomic RNA. Translation: AAP97882.1.
AP006557 Genomic RNA. Translation: BAC81348.1.
AP006558 Genomic RNA. Translation: BAC81362.1.
AP006559 Genomic RNA. Translation: BAC81376.1.
AP006560 Genomic RNA. Translation: BAC81390.1.
AP006561 Genomic RNA. Translation: BAC81404.1.
AY323977 Genomic RNA. Translation: AAP72986.1.
AY362698 Genomic RNA. No translation available.
AY362699 Genomic RNA. No translation available.
AY427439 Genomic RNA. Translation: AAQ94060.1.
AY463059 Genomic RNA. Translation: AAR86788.1.
AY525636 Genomic RNA. Translation: AAS10463.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY278741 Genomic RNA. Translation: AAP13441.1.
AY274119 Genomic RNA. Translation: AAP41037.1.
AY282752 Genomic RNA. Translation: AAP30713.1.
AY278554 Genomic RNA. Translation: AAP13567.1.
AY278491 Genomic RNA. No translation available.
AY304495 Genomic RNA. No translation available.
AY304492 Genomic RNA. No translation available.
AY278487 Genomic RNA. No translation available.
AY278488 Genomic RNA. Translation: AAP30030.1.
AY278490 Genomic RNA. No translation available.
AY279354 Genomic RNA. No translation available.
AY278489 Genomic RNA. Translation: AAP51227.1.
AY283794 Genomic RNA. No translation available.
AY283795 Genomic RNA. No translation available.
AY283796 Genomic RNA. No translation available.
AY283797 Genomic RNA. No translation available.
AY283798 Genomic RNA. No translation available.
AY291451 Genomic RNA. Translation: AAP37017.1.
AY310120 Genomic RNA. Translation: AAP50485.1.
AY291315 Genomic RNA. Translation: AAP33697.1.
AY304486 Genomic RNA. No translation available.
AY321118 Genomic RNA. No translation available.
AY323976 mRNA. Translation: AAP73417.1.
AY322207 Genomic RNA. Translation: AAP82968.1.
AY338174 Genomic RNA. Translation: AAQ01597.1.
AY338175 Genomic RNA. Translation: AAQ01609.1.
AY348314 Genomic RNA. Translation: AAP97882.1.
AP006557 Genomic RNA. Translation: BAC81348.1.
AP006558 Genomic RNA. Translation: BAC81362.1.
AP006559 Genomic RNA. Translation: BAC81376.1.
AP006560 Genomic RNA. Translation: BAC81390.1.
AP006561 Genomic RNA. Translation: BAC81404.1.
AY323977 Genomic RNA. Translation: AAP72986.1.
AY362698 Genomic RNA. No translation available.
AY362699 Genomic RNA. No translation available.
AY427439 Genomic RNA. Translation: AAQ94060.1.
AY463059 Genomic RNA. Translation: AAR86788.1.
AY525636 Genomic RNA. Translation: AAS10463.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Q4Zmodel-A17-680[»]
1T7Gmodel-A/C/E17-680[»]
B/D/F737-1026[»]
1U4Kmodel-D764-1089[»]
1WNCX-ray2.80A/B/C/D/E/F900-948[»]
A/B/C/D/E/F1144-1185[»]
1WYYX-ray2.20A/B885-981[»]
A/B1145-1189[»]
1XJPmodel-A17-680[»]
1ZV7X-ray1.70A/B1150-1193[»]
1ZV8X-ray1.94A/C/E/G/I/K901-950[»]
B/D/F/H/J/L1150-1185[»]
1ZVBX-ray1.70A/B/C940-973[»]
2AJFX-ray2.90E/F323-502[»]
2BEQX-ray1.60A/B/C914-949[»]
D/E/F1148-1193[»]
2BEZX-ray1.60C896-972[»]
F1142-1183[»]
2DD8X-ray2.30S317-518[»]
2FXPNMR-A/B/C1141-1193[»]
2GHVX-ray2.20C/E317-510[»]
2GHWX-ray2.30A/C317-510[»]
2RUMNMR-A770-788[»]
2RUNNMR-A1185-1202[»]
2RUONMR-A873-888[»]
3BGFX-ray3.00A/S318-510[»]
3D0GX-ray2.80E/F324-502[»]
3D0HX-ray3.10E/F324-502[»]
3D0IX-ray2.90E/F324-502[»]
3SCIX-ray2.90E/F306-527[»]
3SCJX-ray3.00E/F323-502[»]
3SCKX-ray3.00E/F324-502[»]
3SCLX-ray3.00E/F324-502[»]
ProteinModelPortaliP59594.
SMRiP59594. Positions 321-512, 896-972, 1148-1193.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-29105N.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP59594.

Family and domain databases

Gene3Di1.20.5.790. 1 hit.
InterProiIPR002552. Corona_S2.
IPR027400. S_HR2.
IPR032500. Spike_N.
IPR018548. Spike_rcpt-bd.
[Graphical view]
PfamiPF01601. Corona_S2. 1 hit.
PF16451. Spike_NTD. 1 hit.
PF09408. Spike_rec_bind. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. 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. "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.
  5. "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.
  6. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Isolate BJ01, Isolate BJ02, Isolate BJ03, Isolate BJ04 and Isolate GD01.
  7. "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.
  8. "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.
  9. "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.
  10. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Isolate Frankfurt 1.
  11. "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.
  12. "SARS coronavirus ZJ01 isolate spike glycoprotein."
    Cong L.-M., Ding G.-Q., Lu Y.-Y., Weng J.-Q., Yan J.-Y., Hu N.-P., Wo J.-E., Chen S.-Y., Zhang Y.-J., Mei L.-L., Wang Z.-G., Yao J., Zhu H.-P., Lu Q.-Y., Li M.-H., Gong L.-M., Shi W., Li L.-J.
    Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Isolate ZJ01.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. "Analysis of SARS coronavirus genome in Shanghai isolates."
    Yuan Z., Zhang X., Hu Y., Lan S., Wang H., Zhou Z., Wen Y.
    Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Isolate Shanghai QXC1.
  20. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Isolate GD03.
  21. "Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus."
    Li W., Moore M.J., Vasilieva N., Sui J., Wong S.-K., Berne M.A., Somasundaran M., Sullivan J.L., Luzuriaga K., Greenough T.C., Choe H., Farzan M.
    Nature 426:450-454(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HUMAN ACE2, CHARACTERIZATION OF CELLULAR RECEPTOR.
  22. "A 193-amino acid fragment of the SARS coronavirus S protein efficiently binds angiotensin-converting enzyme 2."
    Wong S.K., Li W., Moore M.J., Choe H., Farzan M.
    J. Biol. Chem. 279:3197-3201(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HUMAN ACE2.
  23. "Characterization of the heptad repeat regions, HR1 and HR2, and design of a fusion core structure model of the spike protein from severe acute respiratory syndrome (SARS) coronavirus."
    Xu Y., Zhu J., Liu Y., Lou Z., Yuan F., Liu Y., Cole D.K., Ni L., Su N., Qin L., Li X., Bai Z., Bell J.I., Pang H., Tien P., Gao G.F., Rao Z.
    Biochemistry 43:14064-14071(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION OF HEPTAD REPEAT REGIONS.
  24. "The spike protein of severe acute respiratory syndrome (SARS) is cleaved in virus infected Vero-E6 cells."
    Wu X.D., Shang B., Yang R.F., Yu H., Ma Z.H., Shen X., Ji Y.Y., Lin Y., Wu Y.D., Lin G.M., Tian L., Gan X.Q., Yang S., Jiang W.H., Dai E.H., Wang X.Y., Jiang H.L., Xie Y.H.
    , Zhu X.L., Pei G., Li L., Wu J.R., Sun B.
    Cell Res. 14:400-406(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: CLEAVAGE.
  25. Cited for: INTERACTION WITH HUMAN CLEC4M/DC-SIGNR, MUTAGENESIS OF CYS-323; CYS-348; GLU-452; ASP-454; ASP-463; CYS-467; CYS-474 AND ASP-480.
  26. "Oligomerization of the SARS-CoV S glycoprotein: dimerization of the N-terminus and trimerization of the ectodomain."
    Xiao X., Feng Y., Chakraborti S., Dimitrov D.S.
    Biochem. Biophys. Res. Commun. 322:93-99(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: HOMOTRIMERIZATION.
  27. "Identification and characterization of the putative fusion peptide of the severe acute respiratory syndrome-associated coronavirus spike protein."
    Sainz B. Jr., Rausch J.M., Gallaher W.R., Garry R.F., Wimley W.C.
    J. Virol. 79:7195-7206(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION OF FUSION PEPTIDE.
  28. "Differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins S, M and E."
    Nal B., Chan C., Kien F., Siu L., Tse J., Chu K., Kam J., Staropoli I., Crescenzo-Chaigne B., Escriou N., van der Werf S., Yuen K.Y., Altmeyer R.
    J. Gen. Virol. 86:1423-1434(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  29. Cited for: CHARACTERIZATION OF VARIANTS ARG-344; SER-360; LYS-479 AND SER-487.
  30. "Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry."
    Simmons G., Gosalia D.N., Rennekamp A.J., Reeves J.D., Diamond S.L., Bates P.
    Proc. Natl. Acad. Sci. U.S.A. 102:11876-11881(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEOLYSIS BY HUMAN CTSL.
  31. "A novel severe acute respiratory syndrome coronavirus protein, U274, is transported to the cell surface and undergoes endocytosis."
    Tan Y.-J., Teng E., Shen S., Tan T.H.P., Goh P.-Y., Fielding B.C., Ooi E.-E., Tan H.-C., Lim S.G., Hong W.
    J. Virol. 78:6723-6734(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ACCESSORY PROTEIN 3A.
  32. "Severe acute respiratory syndrome coronavirus 7a accessory protein is a viral structural protein."
    Huang C., Ito N., Tseng C.-T.K., Makino S.
    J. Virol. 80:7287-7294(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ACCESSORY PROTEIN 7A.
  33. "Furin cleavage of the SARS coronavirus spike glycoprotein enhances cell-cell fusion but does not affect virion entry."
    Follis K.E., York J., Nunberg J.H.
    Virology 350:358-369(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ARG-667 AND LYS-672.
  34. "Palmitoylation of the cysteine-rich endodomain of the SARS-coronavirus spike glycoprotein is important for spike-mediated cell fusion."
    Petit C.M., Chouljenko V.N., Iyer A., Colgrove R., Farzan M., Knipe D.M., Kousoulas K.G.
    Virology 360:264-274(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PALMITOYLATION.
  35. "The cytoplasmic tail of the severe acute respiratory syndrome coronavirus spike protein contains a novel endoplasmic reticulum retrieval signal that binds COPI and promotes interaction with membrane protein."
    McBride C.E., Li J., Machamer C.E.
    J. Virol. 81:2418-2428(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENDOPLASMIC RETICULUM RETENTION MOTIF, MUTAGENESIS OF LYS-1251 AND HIS-1253.
  36. "Crystal structure of severe acute respiratory syndrome coronavirus spike protein fusion core."
    Xu Y., Lou Z., Liu Y., Pang H., Tien P., Gao G.F., Rao Z.
    J. Biol. Chem. 279:49414-49419(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 900-948.
  37. "Structure of a proteolytically resistant core from the severe acute respiratory syndrome coronavirus S2 fusion protein."
    Supekar V.M., Bruckmann C., Ingallinella P., Bianchi E., Pessi A., Carfi A.
    Proc. Natl. Acad. Sci. U.S.A. 101:17958-17963(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 895-972 AND 1142-1180.
  38. Cited for: 3D-STRUCTURE MODELING OF 17-680.
  39. "Structure of SARS coronavirus spike receptor-binding domain complexed with receptor."
    Li F., Li W., Farzan M., Harrison S.C.
    Science 309:1864-1868(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 323-502 IN COMPLEX WITH HUMAN ACE2.
  40. "Structures and polymorphic interactions of two heptad-repeat regions of the SARS virus S2 protein."
    Deng Y., Liu J., Zheng Q., Yong W., Lu M.
    Structure 14:889-899(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 1150-1193.

Entry informationi

Entry nameiSPIKE_CVHSA
AccessioniPrimary (citable) accession number: P59594
Secondary accession number(s): Q6QU82
, Q7T696, Q7TA19, Q7TFA2, Q7TFB1, Q80BV6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: April 23, 2003
Last modified: December 9, 2015
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

Tor2 is the prototype of the virus isolated during the severe SARS outbreak in 2002-2003. GD03 has been isolated from the second mild SARS outbreak in winter 2003-2004. SZ3 has been isolated from palm civet, the presumed animal reservoir. The spike proteins from those three isolates display a strong affinity for palm civet ACE2 receptor, whereas only the Tor2 spike protein efficiently binds human ACE2. This may explain the high pathogenicity of Tor2 virus, whose spike is highly adapted to the human host. Therefore, the lack of severity of disease during the 2003-2004 outbreak could be due to the incomplete adaptation of GD03 virus to bind human ACE2. Mutation Asn-479 and Thr-487 in palm civet coronavirus seems necessary and sufficient for the virus to acquire the ability to efficiently infect humans.

Caution

Cleavage into S1 and S2 remains controversial, since biochemical evidence for this proteolytic cleavage is largely negative.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.