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Protein

Spike glycoprotein

Gene

S

Organism
Avian infectious bronchitis virus (strain Beaudette) (IBV)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Spike protein S1: attaches the virion to the host cell membrane by interacting with sialic acids, initiating the infection.UniRule annotation2 Publications
Spike protein S2: mediates fusion of the virion and cellular membranes by acting as 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.UniRule annotation
Spike protein S2': Acts as a viral fusion peptide after S2 cleavage occurring upon virus endocytosis.UniRule annotation

GO - Biological processi

Keywordsi

Biological processFusion 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 endocytosis by host, Virus entry into host cell

Names & Taxonomyi

Protein namesi
Recommended name:
Spike glycoproteinUniRule annotation
Short name:
S glycoproteinUniRule annotation
Alternative name(s):
E2UniRule annotation
Peplomer proteinUniRule annotation
Cleaved into the following 3 chains:
Spike protein S1UniRule annotation
Spike protein S2UniRule annotation
Spike protein S2'UniRule annotation
Gene namesi
Name:SUniRule annotation
ORF Names:2
OrganismiAvian infectious bronchitis virus (strain Beaudette) (IBV)
Taxonomic identifieri11122 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageNidoviralesCoronaviridaeCoronavirinaeGammacoronavirus
Virus hostiGallus gallus (Chicken) [TaxID: 9031]
Proteomesi
  • UP000006717 Componenti: Genome

Subcellular locationi

Spike protein S2 :
  • Virion membrane UniRule annotation; Single-pass type I membrane protein UniRule annotation
  • Host endoplasmic reticulum-Golgi intermediate compartment membrane UniRule annotation; Single-pass type I membrane protein UniRule annotation
  • Note: Accumulates in the endoplasmic reticulum-Golgi intermediate compartment, where it participates in virus particle assembly. Some S oligomers may be transported to the plasma membrane, where they may mediate cell-cell fusion.UniRule annotation
Spike protein S1 :
  • Virion membrane UniRule annotation; Peripheral membrane protein UniRule annotation
  • Host endoplasmic reticulum-Golgi intermediate compartment membrane UniRule annotation; Peripheral membrane protein UniRule annotation
  • Note: Accumulates in the endoplasmic reticulum-Golgi intermediate compartment, where it participates in virus particle assembly. Some S oligomers may be transported to the plasma membrane, where they may mediate cell-cell fusion. S1 is not anchored to the viral envelope, but associates with the extravirion surface through its binding to S2.UniRule annotation

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini19 – 1095ExtracellularUniRule annotationAdd BLAST1077
Transmembranei1096 – 1116HelicalUniRule annotationAdd BLAST21
Topological domaini1117 – 1162CytoplasmicUniRule annotationAdd BLAST46

GO - Cellular componenti

Keywords - Cellular componenti

Host membrane, Membrane, Viral envelope protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1159K → A: Localizes exclusively to the cell membrane. 1 Publication1
Mutagenesisi1160K → A: Localizes exclusively to the cell membrane. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 18UniRule annotationAdd BLAST18
ChainiPRO_000003716219 – 1162Spike glycoproteinUniRule annotationAdd BLAST1144
ChainiPRO_000003716319 – 537Spike protein S1UniRule annotation1 PublicationAdd BLAST519
ChainiPRO_0000037164538 – 1162Spike protein S2UniRule annotation1 PublicationAdd BLAST625
ChainiPRO_0000444092691 – 1162Spike protein S2'UniRule annotation1 PublicationAdd BLAST472

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi51N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi77N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi103N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi144N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi163N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi178N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi212N-linked (GlcNAc...) asparagine; by hostUniRule annotation1 Publication1
Glycosylationi237N-linked (GlcNAc...) asparagine; by hostUniRule annotation1 Publication1
Glycosylationi247N-linked (GlcNAc...) asparagine; by hostUniRule annotation1 Publication1
Glycosylationi264N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi276N-linked (GlcNAc...) asparagine; by hostUniRule annotation1 Publication1
Glycosylationi306N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi425N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi447N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi513N-linked (GlcNAc...) asparagine; by hostUniRule annotation1 Publication1
Glycosylationi530N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi579N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi591N-linked (GlcNAc...) asparagine; by hostUniRule annotation1 Publication1
Glycosylationi669N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi676N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi714N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi947N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi960N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi979N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi1014N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi1038N-linked (GlcNAc...) asparagine; by hostUniRule annotation1
Glycosylationi1051N-linked (GlcNAc...) asparagine; by hostUniRule annotation1 Publication1
Glycosylationi1074N-linked (GlcNAc...) asparagine; by hostUniRule annotation1 Publication1

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host cell furin or furin-like protease to yield the mature S1 and S2 proteins. The cleavage site between S1 and S2 requires the optimal sequence [KR]-X-[KR]-R. Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor.UniRule annotation1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei537 – 538Cleavage; by host furinUniRule annotation1 Publication2
Sitei690 – 691Cleavage; by host furinUniRule annotation1 Publication2

Keywords - PTMi

Cleavage on pair of basic residues, Glycoprotein

Proteomic databases

PRIDEiP11223

Interactioni

Subunit structurei

Homotrimer; each monomer consists of a S1 and a S2 subunit. The resulting peplomers protrude from the virus surface as spikes.UniRule annotation

Protein-protein interaction databases

ELMiP11223

Structurei

3D structure databases

ProteinModelPortaliP11223
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili822 – 866UniRule annotationAdd BLAST45
Coiled coili1055 – 1083UniRule annotationAdd BLAST29

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1159 – 1162Di-lysine motifUniRule annotation4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1120 – 1137Cys-richAdd BLAST18

Domaini

The di-lysine motif confers endoplasmic reticulum localization for type I membrane proteins.UniRule annotation

Sequence similaritiesi

Belongs to the gammacoronaviruses spike protein family.UniRule annotation

Keywords - Domaini

Coiled coil, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

KOiK19254
OrthoDBiVOG0900000Z

Family and domain databases

Gene3Di1.20.5.790, 1 hit
HAMAPiMF_04098 GAMMA_CORONA_SPIKE, 1 hit
InterProiView protein in InterPro
IPR002551 Corona_S1
IPR002552 Corona_S2
IPR027400 S_HR2
PfamiView protein in Pfam
PF01600 Corona_S1, 1 hit
PF01601 Corona_S2, 1 hit

Sequencei

Sequence statusi: Complete.

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

P11223-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLVTPLLLVT LLCALCSAVL YDSSSYVYYY QSAFRPPSGW HLQGGAYAVV
60 70 80 90 100
NISSEFNNAG SSSGCTVGII HGGRVVNASS IAMTAPSSGM AWSSSQFCTA
110 120 130 140 150
HCNFSDTTVF VTHCYKHGGC PLTGMLQQNL IRVSAMKNGQ LFYNLTVSVA
160 170 180 190 200
KYPTFRSFQC VNNLTSVYLN GDLVYTSNET IDVTSAGVYF KAGGPITYKV
210 220 230 240 250
MREVKALAYF VNGTAQDVIL CDGSPRGLLA CQYNTGNFSD GFYPFTNSSL
260 270 280 290 300
VKQKFIVYRE NSVNTTCTLH NFIFHNETGA NPNPSGVQNI QTYQTKTAQS
310 320 330 340 350
GYYNFNFSFL SSFVYKESNF MYGSYHPSCK FRLETINNGL WFNSLSVSIA
360 370 380 390 400
YGPLQGGCKQ SVFKGRATCC YAYSYGGPSL CKGVYSGELD HNFECGLLVY
410 420 430 440 450
VTKSGGSRIQ TATEPPVITQ NNYNNITLNT CVDYNIYGRT GQGFITNVTD
460 470 480 490 500
SAVSYNYLAD AGLAILDTSG SIDIFVVQGE YGLNYYKVNP CEDVNQQFVV
510 520 530 540 550
SGGKLVGILT SRNETGSQLL ENQFYIKITN GTRRFRRSIT ENVANCPYVS
560 570 580 590 600
YGKFCIKPDG SIATIVPKQL EQFVAPLFNV TENVLIPNSF NLTVTDEYIQ
610 620 630 640 650
TRMDKVQINC LQYVCGSSLD CRKLFQQYGP VCDNILSVVN SVGQKEDMEL
660 670 680 690 700
LNFYSSTKPA GFNTPVLSNV STGEFNISLL LTNPSSRRKR SLIEDLLFTS
710 720 730 740 750
VESVGLPTND AYKNCTAGPL GFFKDLACAR EYNGLLVLPP IITAEMQALY
760 770 780 790 800
TSSLVASMAF GGITAAGAIP FATQLQARIN HLGITQSLLL KNQEKIAASF
810 820 830 840 850
NKAIGHMQEG FRSTSLALQQ IQDVVSKQSA ILTETMASLN KNFGAISSVI
860 870 880 890 900
QEIYQQFDAI QANAQVDRLI TGRLSSLSVL ASAKQAEYIR VSQQRELATQ
910 920 930 940 950
KINECVKSQS IRYSFCGNGR HVLTIPQNAP NGIVFIHFSY TPDSFVNVTA
960 970 980 990 1000
IVGFCVKPAN ASQYAIVPAN GRGIFIQVNG SYYITARDMY MPRAITAGDV
1010 1020 1030 1040 1050
VTLTSCQANY VSVNKTVITT FVDNDDFDFN DELSKWWNDT KHELPDFDKF
1060 1070 1080 1090 1100
NYTVPILDID SEIDRIQGVI QGLNDSLIDL EKLSILKTYI KWPWYVWLAI
1110 1120 1130 1140 1150
AFATIIFILI LGWVFFMTGC CGCCCGCFGI MPLMSKCGKK SSYYTTFDND
1160
VVTEQYRPKK SV
Length:1,162
Mass (Da):128,047
Last modified:July 1, 1989 - v1
Checksum:i0BAAD58113C8EBD5
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti122L → I in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti130L → F in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti364K → R in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti405G → D in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti421N → H in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti623K → N in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti683N → T in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti689K → R in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti692L → V in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti709N → D in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti723F → L in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1
Natural varianti1012S → I in strain: Isolate Vero cell-adapted p36 and Isolate Vero cell-adapted p65. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M95169 Genomic RNA Translation: AAA70235.1
X02342 Genomic RNA Translation: CAA26201.1
DQ001342 mRNA Translation: AAY21248.1
DQ001339 Genomic RNA Translation: AAY24433.1
PIRiS14939
RefSeqiNP_040831.1, NC_001451.1

Genome annotation databases

GeneIDi1489741
KEGGivg:1489741

Similar proteinsi

Entry informationi

Entry nameiSPIKE_IBVB
AccessioniPrimary (citable) accession number: P11223
Secondary accession number(s): P05134, Q4ZJS1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: May 23, 2018
This is version 107 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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