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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
 
 
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