SPIKE_IBVM
ID SPIKE_IBVM Reviewed; 1162 AA.
AC P12651; Q0GNB8; Q5I5X9;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1989, sequence version 1.
DT 25-MAY-2022, entry version 117.
DE RecName: Full=Spike glycoprotein {ECO:0000255|HAMAP-Rule:MF_04098};
DE Short=S glycoprotein {ECO:0000255|HAMAP-Rule:MF_04098};
DE AltName: Full=E2 {ECO:0000255|HAMAP-Rule:MF_04098};
DE AltName: Full=Peplomer protein {ECO:0000255|HAMAP-Rule:MF_04098};
DE Contains:
DE RecName: Full=Spike protein S1 {ECO:0000255|HAMAP-Rule:MF_04098};
DE Contains:
DE RecName: Full=Spike protein S2 {ECO:0000255|HAMAP-Rule:MF_04098};
DE Contains:
DE RecName: Full=Spike protein S2' {ECO:0000255|HAMAP-Rule:MF_04098};
DE Flags: Precursor;
GN Name=S {ECO:0000255|HAMAP-Rule:MF_04098}; ORFNames=2;
OS Avian infectious bronchitis virus (strain M41) (IBV).
OC Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae;
OC Gammacoronavirus; Igacovirus.
OX NCBI_TaxID=11127;
OH NCBI_TaxID=9031; Gallus gallus (Chicken).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=2429473; DOI=10.1016/0168-1702(86)90022-5;
RA Niesters H.G.M., Lenstra J.A., Spaan W.J.M., Zijderveld A.J.,
RA Bleumink-Pluym N.M.C., Hong F., van Scharrenburg G.J.M., Horzinek M.C.,
RA van der Zeijst B.A.M.;
RT "The peplomer protein sequence of the M41 strain of coronavirus IBV and its
RT comparison with Beaudette strains.";
RL Virus Res. 5:253-263(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RA Mondal S.P., Buckles E.L.;
RT "Avian infectious bronchitis virus strain M41.";
RL Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=16934878; DOI=10.1016/j.jviromet.2006.07.018;
RA Callison S.A., Hilt D.A., Boynton T.O., Sample B.F., Robison R.,
RA Swayne D.E., Jackwood M.W.;
RT "Development and evaluation of a real-time Taqman RT-PCR assay for the
RT detection of infectious bronchitis virus from infected chickens.";
RL J. Virol. Methods 138:60-65(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Madu I.G., Chu V.C., Lee H., Regan A.D., Bauman B.E., Whittaker G.R.;
RT "Heparan sulfate is a selective attachment factor for the avian coronavirus
RT IBV Beaudette.";
RL Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: [Spike protein S1]: Attaches the virion to the host cell
CC membrane by interacting with sialic acids, initiating the infection.
CC {ECO:0000255|HAMAP-Rule:MF_04098}.
CC -!- FUNCTION: [Spike protein S2]: Mediates fusion of the virion and
CC cellular membranes by acting as a class I viral fusion protein. Under
CC the current model, the protein has at least 3 conformational states:
CC pre-fusion native state, pre-hairpin intermediate state, and post-
CC fusion hairpin state. During viral and target cell membrane fusion, the
CC coiled coil regions (heptad repeats) assume a trimer-of-hairpins
CC structure, positioning the fusion peptide in close proximity to the C-
CC terminal region of the ectodomain. The formation of this structure
CC appears to drive apposition and subsequent fusion of viral and target
CC cell membranes. {ECO:0000255|HAMAP-Rule:MF_04098}.
CC -!- FUNCTION: [Spike protein S2']: Acts as a viral fusion peptide after S2
CC cleavage occurring upon virus endocytosis. {ECO:0000255|HAMAP-
CC Rule:MF_04098}.
CC -!- SUBUNIT: Homotrimer; each monomer consists of a S1 and a S2 subunit.
CC The resulting peplomers protrude from the virus surface as spikes.
CC {ECO:0000255|HAMAP-Rule:MF_04098}.
CC -!- SUBCELLULAR LOCATION: [Spike protein S2]: Virion membrane
CC {ECO:0000255|HAMAP-Rule:MF_04098}; Single-pass type I membrane protein
CC {ECO:0000255|HAMAP-Rule:MF_04098}. Host endoplasmic reticulum-Golgi
CC intermediate compartment membrane {ECO:0000255|HAMAP-Rule:MF_04098};
CC Single-pass type I membrane protein {ECO:0000255|HAMAP-Rule:MF_04098}.
CC Note=Accumulates in the endoplasmic reticulum-Golgi intermediate
CC compartment, where it participates in virus particle assembly. Some S
CC oligomers may be transported to the plasma membrane, where they may
CC mediate cell-cell fusion. {ECO:0000255|HAMAP-Rule:MF_04098}.
CC -!- SUBCELLULAR LOCATION: [Spike protein S1]: Virion membrane
CC {ECO:0000255|HAMAP-Rule:MF_04098}; Peripheral membrane protein
CC {ECO:0000255|HAMAP-Rule:MF_04098}. Host endoplasmic reticulum-Golgi
CC intermediate compartment membrane {ECO:0000255|HAMAP-Rule:MF_04098};
CC Peripheral membrane protein {ECO:0000255|HAMAP-Rule:MF_04098}.
CC Note=Accumulates in the endoplasmic reticulum-Golgi intermediate
CC compartment, where it participates in virus particle assembly. Some S
CC oligomers may be transported to the plasma membrane, where they may
CC mediate cell-cell fusion. S1 is not anchored to the viral envelope, but
CC associates with the extravirion surface through its binding to S2.
CC {ECO:0000255|HAMAP-Rule:MF_04098}.
CC -!- DOMAIN: The di-lysine motif confers endoplasmic reticulum localization
CC for type I membrane proteins. {ECO:0000255|HAMAP-Rule:MF_04098}.
CC -!- PTM: Specific enzymatic cleavages in vivo yield mature proteins. The
CC precursor is processed into S1 and S2 by host cell furin or furin-like
CC protease to yield the mature S1 and S2 proteins. The cleavage site
CC between S1 and S2 requires the optimal sequence [KR]-X-[KR]-R.
CC Additionally, a second cleavage leads to the release of a fusion
CC peptide after viral attachment to host cell receptor.
CC {ECO:0000255|HAMAP-Rule:MF_04098}.
CC -!- SIMILARITY: Belongs to the gammacoronaviruses spike protein family.
CC {ECO:0000255|HAMAP-Rule:MF_04098}.
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DR EMBL; M21883; AAA66575.1; -; Genomic_RNA.
DR EMBL; DQ834384; ABI26423.1; -; Genomic_RNA.
DR EMBL; AY851295; AAW33786.1; -; Genomic_RNA.
DR EMBL; DQ830980; ABH01141.1; -; Genomic_DNA.
DR PIR; S07421; S07421.
DR SMR; P12651; -.
DR Proteomes; UP000007642; Genome.
DR Proteomes; UP000096468; Genome.
DR GO; GO:0044173; C:host cell endoplasmic reticulum-Golgi intermediate compartment membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0019031; C:viral envelope; IEA:UniProtKB-KW.
DR GO; GO:0055036; C:virion membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0075509; P:endocytosis involved in viral entry into host cell; IEA:UniProtKB-KW.
DR GO; GO:0039654; P:fusion of virus membrane with host endosome membrane; IEA:UniProtKB-KW.
DR GO; GO:0019064; P:fusion of virus membrane with host plasma membrane; IEA:InterPro.
DR GO; GO:0046813; P:receptor-mediated virion attachment to host cell; IEA:InterPro.
DR HAMAP; MF_04098; GAMMA_CORONA_SPIKE; 1.
DR InterPro; IPR043607; CoV_S1_C.
DR InterPro; IPR043473; S2_sf_CoV.
DR InterPro; IPR002552; Spike_S2_CoV.
DR InterPro; IPR043614; Spike_S2_CoV_C.
DR InterPro; IPR044873; Spike_S2_CoV_HR1.
DR InterPro; IPR044874; Spike_S2_CoV_HR2.
DR Pfam; PF19209; CoV_S1_C; 1.
DR Pfam; PF01601; CoV_S2; 1.
DR Pfam; PF19214; CoV_S2_C; 1.
DR SUPFAM; SSF111474; SSF111474; 2.
DR PROSITE; PS51923; COV_S2_HR1; 1.
PE 3: Inferred from homology;
KW Cleavage on pair of basic residues; Coiled coil;
KW Fusion of virus membrane with host endosomal membrane;
KW Fusion of virus membrane with host membrane; Glycoprotein; Host membrane;
KW Host-virus interaction; Membrane; Signal; Transmembrane;
KW Transmembrane helix; Viral attachment to host cell; Viral envelope protein;
KW Viral penetration into host cytoplasm; Virion; Virulence;
KW Virus endocytosis by host; Virus entry into host cell.
FT SIGNAL 1..18
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CHAIN 19..1162
FT /note="Spike glycoprotein"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT /id="PRO_0000037171"
FT CHAIN 19..537
FT /note="Spike protein S1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT /id="PRO_0000037172"
FT CHAIN 538..1162
FT /note="Spike protein S2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT /id="PRO_0000037173"
FT CHAIN 691..1162
FT /note="Spike protein S2'"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT /id="PRO_0000444095"
FT TOPO_DOM 19..1095
FT /note="Extracellular"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT TRANSMEM 1096..1116
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT TOPO_DOM 1117..1162
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT REGION 769..874
FT /note="Heptad repeat 1 (HR1)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01271"
FT REGION 1024..1105
FT /note="Heptad repeat 2 (HR2)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01272"
FT COILED 822..866
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT COILED 1055..1083
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT MOTIF 1159..1162
FT /note="Di-lysine motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT SITE 537..538
FT /note="Cleavage; by host furin"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT SITE 690..691
FT /note="Cleavage; by host furin"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 51
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 77
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 103
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 144
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 163
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 178
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 212
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 237
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 247
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 264
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 271
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 276
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 306
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 425
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 447
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 513
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 530
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 579
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 591
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 669
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 676
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 714
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 947
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 960
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 979
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 1014
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 1038
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 1051
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT CARBOHYD 1074
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04098"
FT VARIANT 203
FT /note="K -> E"
FT VARIANT 291
FT /note="L -> Q"
FT VARIANT 823
FT /note="D -> H"
FT VARIANT 829
FT /note="S -> N"
FT VARIANT 849
FT /note="V -> L"
SQ SEQUENCE 1162 AA; 128078 MW; 3C9CC70938492DDA CRC64;
MLVTPLLLVT LLCVLCSAAL YDSSSYVYYY QSAFRPPNGW HLHGGAYAVV NISSESNNAG
SSPGCIVGTI HGGRVVNASS IAMTAPSSGM AWSSSQFCTA HCNFSDTTVF VTHCYKYDGC
PITGMLQKNF LRVSAMKNGQ LFYNLTVSVA KYPTFKSFQC VNNLTSVYLN GDLVYTSNET
TDVTSAGVYF KAGGPITYKV MRKVKALAYF VNGTAQDVIL CDGSPRGLLA CQYNTGNFSD
GFYPFINSSL VKQKFIVYRE NSVNTTFTLH NFTFHNETGA NPNPSGVQNI LTYQTQTAQS
GYYNFNFSFL SSFVYKESNF MYGSYHPSCN FRLETINNGL WFNSLSVSIA YGPLQGGCKQ
SVFSGRATCC YAYSYGGPSL CKGVYSGELD LNFECGLLVY VTKSGGSRIQ TATEPPVITR
HNYNNITLNT CVDYNIYGRT GQGFITNVTD SAVSYNYLAD AGLAILDTSG SIDIFVVQGE
YGLTYYKVNP CEDVNQQFVV SGGKLVGILT SRNETGSQLL ENQFYIKITN GTRRFRRSIT
ENVANCPYVS YGKFCIKPDG SIATIVPKQL EQFVAPLLNV TENVLIPNSF NLTVTDEYIQ
TRMDKVQINC LQYVCGNSLD CRDLFQQYGP VCDNILSVVN SIGQKEDMEL LNFYSSTKPA
GFNTPFLSNV STGEFNISLL LTTPSSPRRR SFIEDLLFTS VESVGLPTDD AYKNCTAGPL
GFLKDLACAR EYNGLLVLPP IITAEMQTLY TSSLVASMAF GGITAAGAIP FATQLQARIN
HLGITQSLLL KNQEKIAASF NKAIGRMQEG FRSTSLALQQ IQDVVNKQSA ILTETMASLN
KNFGAISSVI QEIYQQLDAI QANAQVDRLI TGRLSSLSVL ASAKQAEHIR VSQQRELATQ
KINECVKSQS IRYSFCGNGR HVLTIPQNAP NGIVFIHFSY TPDSFVNVTA IVGFCVKPAN
ASQYAIVPAN GRGIFIQVNG SYYITARDMY MPRAITAGDI VTLTSCQANY VSVNKTVITT
FVDNDDFDFN DELSKWWNDT KHELPDFDKF NYTVPILDID SEIDRIQGVI QGLNDSLIDL
EKLSILKTYI KWPWYVWLAI AFATIIFILI LGWVFFMTGC CGCCCGCFGI MPLMSKCGKK
SSYYTTFDND VVTEQNRPKK SV
