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Protein

Spike glycoprotein

Gene

S

Organism
Bat coronavirus Rp3/2004 (BtCoV/Rp3/2004) (SARS-like coronavirus Rp3)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

S1 is responsible for binding to the receptor on target cells. Binding to the receptor and internalization of the virus into the endosomes of the host cell probably induce conformational changes in the S glycoprotein. Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes (By similarity).By similarity
S2 is a class I viral fusion protein. Under the current model, the protein has at least 3 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 (By similarity).By similarity

Miscellaneous

Bat coronavirus rp3 is highly similar to SARS-CoV (SARS-like).

GO - Biological processi

Keywordsi

Biological processFusion 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
OrganismiBat coronavirus Rp3/2004 (BtCoV/Rp3/2004) (SARS-like coronavirus Rp3)
Taxonomic identifieri349344 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageNidoviralesCoronaviridaeCoronavirinaeBetacoronavirus
Virus hostiRhinolophus ferrumequinum (Greater horseshoe bat) [TaxID: 59479]
Rhinolophus macrotis (Big-eared horseshoe bat) [TaxID: 196889]
Rhinolophus pearsonii [TaxID: 188571]
Rhinolophus sinicus (Chinese rufous horseshoe bat) [TaxID: 89399]
Proteomesi
  • UP000006570 Componenti: Genome

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini16 – 1181ExtracellularSequence analysisAdd BLAST1166
Transmembranei1182 – 1202HelicalSequence analysisAdd BLAST21
Topological domaini1203 – 1241CytoplasmicSequence analysisAdd BLAST39

GO - Cellular componenti

Keywords - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 15Sequence analysisAdd BLAST15
ChainiPRO_000004307616 – 1241Spike glycoproteinAdd BLAST1226
ChainiPRO_000004307716 – 653Spike protein S1Sequence analysisAdd BLAST638
ChainiPRO_0000043078654 – 1241Spike protein S2Sequence analysisAdd BLAST588

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi65N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi115N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi124N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi125N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi162N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi231N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi273N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi298N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi322N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi334N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi361N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi575N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi588N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi629N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi677N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi685N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi769N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi1042N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi1066N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi1102N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi1126N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi1141N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi1162N-linked (GlcNAc...) asparagine; by hostSequence analysis1

Post-translational modificationi

Digested by cathepsin CTSL within endosomes.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei653 – 654CleavageSequence analysis2

Keywords - PTMi

Glycoprotein

Interactioni

Subunit structurei

Homotrimer.By similarity

Structurei

Secondary structure

11241
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi913 – 948Combined sources36

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZVAX-ray1.50A912-948[»]
A1135-1169[»]
ProteinModelPortaliQ3I5J5.
SMRiQ3I5J5.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ3I5J5.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni756 – 774Fusion peptideSequence analysisAdd BLAST19
Regioni888 – 938Heptad repeat 1Add BLAST51
Regioni1131 – 1170Heptad repeat 2Add BLAST40

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili917 – 961Sequence analysisAdd BLAST45
Coiled coili1143 – 1171Sequence analysisAdd BLAST29

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1237 – 1241KxHxxBy similarity5

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1203 – 1222Cys-richAdd BLAST20

Domaini

The KxHxx motif seems to function as an ER retrieval signal.By similarity

Sequence similaritiesi

Belongs to the coronaviruses spike protein family.Curated

Keywords - Domaini

Coiled coil, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

OrthoDBiVOG0900000Z.

Family and domain databases

Gene3Di1.20.5.790. 1 hit.
InterProiView protein in InterPro
IPR002552. Corona_S2.
IPR027400. S_HR2.
IPR032500. Spike_N.
IPR018548. Spike_rcpt-bd.
IPR036326. Spike_rcpt-bd_sf.
PfamiView protein in Pfam
PF01601. Corona_S2. 1 hit.
PF16451. Spike_NTD. 1 hit.
PF09408. Spike_rec_bind. 1 hit.
SUPFAMiSSF143587. SSF143587. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q3I5J5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKILILAFLA SLAKAQEGCG IISRKPQPKM AQVSSSRRGV YYNDDIFRSN
60 70 80 90 100
VLHLTQDYFL PFDSNLTQYF SLNVDSDRFT YFDNPILDFG DGVYFAATEK
110 120 130 140 150
SNVIRGWIFG STFDNTTQSA VIVNNSTHII IRVCNFNLCK EPMYTVSRGA
160 170 180 190 200
QQSSWVYQSA FNCTYDRVEK SFQLDTAPKT GNFKDLREYV FKNRDGFLSV
210 220 230 240 250
YQTYTAVNLP RGLPIGFSVL RPILKLPFGI NITSYRVVMA MFSQTTSNFL
260 270 280 290 300
PESAAYYVGN LKYTTFMLSF NENGTITNAI DCAQNPLAEL KCTIKNFNVS
310 320 330 340 350
KGIYQTSNFR VSPTQEVIRF PNITNRCPFD KVFNATRFPN VYAWERTKIS
360 370 380 390 400
DCVADYTVLY NSTSFSTFKC YGVSPSKLID LCFTSVYADT FLIRSSEVRQ
410 420 430 440 450
VAPGETGVIA DYNYKLPDDF TGCVIAWNTA KQDQGQYYYR SHRKTKLKPF
460 470 480 490 500
ERDLSSDENG VRTLSTYDFY PSVPVAYQAT RVVVLSFELL NAPATVCGPK
510 520 530 540 550
LSTQLVKNQC VNFNFNGLKG TGVLTESSKR FQSFQQFGRD TSDFTDSVRD
560 570 580 590 600
PQTLEILDIS PCSFGGVSVI TPGTNASSEV AVLYQDVNCT DVPAAIHADQ
610 620 630 640 650
LTPAWRVYST GTNVFQTQAG CLIGAEHVNA SYECDIPIGA GICASYHTAS
660 670 680 690 700
TLRSVGQKSI VAYTMSLGAE NSIAYANNSI AIPTNFSISV TTEVMPVSMA
710 720 730 740 750
KTSVDCTMYI CGDSLECSNL LLQYGSFCTQ LNRALSGIAI EQDKNTQEVF
760 770 780 790 800
AQVKQMYKTP AIKDFGGFNF SQILPDPSKP TKRSFIEDLL FNKVTLADAG
810 820 830 840 850
FMKQYGECLG DISARDLICA QKFNGLTVLP PLLTDEMIAA YTAALVSGTA
860 870 880 890 900
TAGWTFGAGS ALQIPFAMQM AYRFNGIGVT QNVLYENQKQ IANQFNKAIS
910 920 930 940 950
QIQESLTTTS TALGKLQDVV NQNAQALNTL VKQLSSNFGA ISSVLNDILS
960 970 980 990 1000
RLDKVEAEVQ IDRLITGRLQ SLQTYVTQQL IRAAEIRASA NLAATKMSEC
1010 1020 1030 1040 1050
VLGQSKRVDF CGKGYHLMSF PQAAPHGVVF LHVTYVPSQE RNFTTAPAIC
1060 1070 1080 1090 1100
HEGKAYFPRE GVFVSNGTSW FITQRNFYSP QIITTDNTFV AGSCDVVIGI
1110 1120 1130 1140 1150
INNTVYDPLQ PELDSFKEEL DKYFKNHTSP DVDLGDISGI NASVVNIQKE
1160 1170 1180 1190 1200
IDRLNEVAKN LNESLIDLQE LGKYEQYIKW PWYVWLGFIA GLIAIVMVTI
1210 1220 1230 1240
LLCCMTSCCS CLKGACSCGS CCKFDEDDSE PVLKGVKLHY T
Length:1,241
Mass (Da):137,560
Last modified:November 8, 2005 - v1
Checksum:i4C55A922A7A463B4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ071615 Genomic RNA. Translation: AAZ67052.1.

Similar proteinsi

Entry informationi

Entry nameiSPIKE_BCRP3
AccessioniPrimary (citable) accession number: Q3I5J5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: November 8, 2005
Last modified: December 20, 2017
This is version 85 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Caution

Cleavage into S1 and S2 remains controversial.Curated

Keywords - Technical termi

3D-structure, Complete proteome