Strain

USA_AVIAN_2004_NC_001451 (Region: USA: Beaudette;  Strain: Avian infectious bronchitis virus, complete genome.;  Date: 2004)

Gene

spike protein

Description

Annotated in NCBI,  spike protein

Location

NC_001451(+):20368-23856

GenBank Accession

NP_040831.1

Full name

Spike glycoprotein      

Alternative Name

E2
Peplomer protein

CDS

ATGTTGGTAACACCTCTTTTACTAGTGACTCTTTTGTGTGCACTATGTAGTGCTGTTTTGTATGACAGTAGTTCTTACGTTTACTACTACCAAAGTGCCTTCAGACCACCTAGTGGTTGGCATTTACAAGGGGGTGCTTATGCGGTAGTTAACATTTCTAGCGAATTTAATAATGCAGGCTCTTCATCAGGGTGTACTGTTGGTATTATTCATGGTGGTCGTGTTGTTAATGCTTCTTCTATAGCTATGACGGCACCGTCATCAGGTATGGCTTGGTCTAGCAGTCAGTTTTGTACTGCACACTGTAATTTTTCAGATACTACAGTGTTTGTTACACATTGTTATAAACATGGTGGGTGTCCTTTAACTGGCATGCTTCAACAGAATCTTATACGTGTTTCTGCTATGAAAAATGGCCAGCTTTTCTATAATTTAACAGTTAGTGTAGCTAAGTACCCTACTTTTAGATCATTTCAGTGTGTTAATAATTTAACATCCGTATATTTAAATGGTGATCTTGTTTACACCTCTAATGAGACCATAGATGTTACATCTGCAGGTGTTTATTTTAAAGCTGGTGGACCTATAACTTATAAAGTTATGAGAGAAGTTAAAGCCCTGGCTTATTTTGTTAATGGTACTGCACAAGATGTTATTTTGTGTGATGGATCACCTAGAGGCTTGTTAGCATGCCAGTATAATACTGGCAATTTTTCAGATGGCTTTTATCCTTTTACTAATAGTAGTTTAGTTAAGCAGAAGTTTATTGTCTATCGTGAAAATAGTGTTAATACTACTTGTACGTTACACAATTTCATTTTTCATAATGAGACTGGCGCCAACCCTAATCCTAGTGGTGTTCAGAATATTCAAACTTACCAAACAAAAACAGCTCAGAGTGGTTATTATAATTTTAATTTTTCCTTTCTGAGTAGTTTTGTTTATAAGGAGTCTAATTTTATGTATGGATCTTATCACCCAAGTTGTAAATTTAGACTAGAAACTATTAATAATGGCTTGTGGTTTAATTCACTTTCAGTTTCAATTGCTTACGGTCCTCTTCAAGGTGGTTGCAAGCAATCTGTCTTTAAAGGTAGAGCAACTTGTTGTTATGCTTATTCATATGGAGGTCCTTCGCTGTGTAAAGGTGTTTATTCAGGTGAGTTAGATCATAATTTTGAATGTGGACTGTTAGTTTATGTTACTAAGAGCGGTGGCTCTCGTATACAAACAGCCACTGAACCGCCAGTTATAACTCAAAACAATTATAATAATATTACTTTAAATACTTGTGTTGATTATAATATATATGGCAGAACTGGCCAAGGTTTTATTACTAATGTGACCGACTCAGCTGTTAGTTATAATTATCTAGCAGACGCAGGTTTGGCTATTTTAGATACATCTGGTTCCATAGACATCTTTGTTGTACAAGGTGAATATGGTCTTAATTATTATAAGGTTAACCCTTGCGAAGATGTCAACCAGCAGTTTGTAGTTTCTGGTGGTAAATTAGTAGGTATTCTTACTTCACGTAATGAGACTGGTTCTCAGCTTCTTGAGAACCAGTTTTACATCAAAATCACTAATGGAACACGTCGTTTTAGACGTTCTATTACTGAAAATGTTGCAAATTGCCCTTATGTTAGTTATGGTAAGTTTTGTATAAAACCTGATGGCTCAATTGCCACAATAGTACCAAAACAATTGGAACAGTTTGTGGCACCTTTATTTAATGTTACTGAAAATGTGCTCATACCTAACAGTTTCAACTTAACTGTTACAGATGAGTACATACAAACGCGTATGGATAAGGTCCAAATTAATTGCCTGCAGTATGTTTGTGGCAGTTCTCTGGATTGTAGAAAGTTGTTTCAACAATATGGGCCTGTTTGCGACAACATATTGTCTGTAGTAAATAGTGTTGGTCAAAAAGAAGATATGGAACTTTTGAATTTCTATTCTTCTACTAAACCGGCTGGTTTTAATACACCAGTTCTTAGTAATGTTAGCACTGGTGAGTTTAATATTTCTCTTCTGTTAACAAATCCTAGTAGTCGTAGAAAGCGTTCTCTTATTGAAGACCTTCTATTTACAAGCGTTGAATCTGTTGGACTACCAACAAATGACGCATATAAAAATTGCACTGCAGGACCTTTAGGCTTTTTTAAGGACCTTGCGTGTGCTCGTGAATATAATGGTTTGCTTGTGTTGCCTCCTATCATAACAGCAGAAATGCAAGCTTTGTATACTAGTTCTCTAGTAGCTTCTATGGCTTTTGGTGGTATTACTGCAGCTGGTGCTATACCTTTTGCCACACAACTGCAGGCTAGAATTAATCACTTGGGTATTACCCAGTCACTTTTGTTGAAGAATCAAGAAAAAATTGCTGCTTCCTTTAATAAGGCCATTGGTCATATGCAGGAAGGTTTTAGAAGTACATCTCTAGCATTACAACAAATTCAAGATGTTGTTAGTAAACAGAGTGCTATTCTTACTGAGACTATGGCATCACTTAATAAAAATTTTGGTGCTATTTCTTCTGTGATTCAAGAAATCTACCAGCAATTTGACGCCATACAAGCAAATGCTCAAGTGGATCGTCTTATAACTGGTAGATTGTCATCACTTTCTGTTTTAGCATCTGCTAAGCAGGCGGAGTATATTAGAGTGTCACAACAGCGTGAGTTAGCTACTCAGAAAATTAATGAGTGTGTTAAGTCACAGTCTATTAGGTACTCCTTTTGTGGTAATGGACGACATGTTCTAACCATACCGCAAAATGCACCTAATGGTATAGTGTTTATACACTTTTCTTATACTCCAGATAGTTTTGTTAATGTTACTGCAATAGTGGGTTTTTGTGTAAAGCCAGCTAATGCTAGTCAGTATGCAATAGTGCCCGCTAATGGTAGGGGTATTTTTATACAAGTTAATGGTAGTTACTACATCACTGCACGAGATATGTATATGCCAAGAGCTATTACTGCAGGAGATGTAGTTACGCTTACTTCTTGTCAAGCAAATTATGTAAGTGTAAATAAGACCGTCATTACTACATTCGTAGACAATGATGATTTTGATTTTAATGACGAATTGTCAAAATGGTGGAATGATACTAAGCATGAGCTACCAGACTTTGACAAATTCAATTACACAGTACCTATACTTGACATTGATAGTGAAATTGATCGTATTCAAGGCGTTATACAGGGTCTTAATGACTCTCTAATAGACCTTGAAAAACTTTCAATACTCAAAACTTATATTAAGTGGCCTTGGTATGTGTGGTTAGCCATAGCTTTTGCCACTATTATCTTCATCTTAATACTAGGATGGGTTTTCTTCATGACTGGTTGTTGTGGTTGTTGTTGTGGATGCTTTGGCATTATGCCTCTAATGAGTAAGTGTGGTAAGAAATCTTCTTATTACACGACTTTTGATAACGATGTGGTAACTGAACAATACAGACCTAAAAAGTCTGTTTGA

Protein

MLVTPLLLVTLLCALCSAVLYDSSSYVYYYQSAFRPPSGWHLQGGAYAVVNISSEFNNAGSSSGCTVGIIHGGRVVNASSIAMTAPSSGMAWSSSQFCTAHCNFSDTTVFVTHCYKHGGCPLTGMLQQNLIRVSAMKNGQLFYNLTVSVAKYPTFRSFQCVNNLTSVYLNGDLVYTSNETIDVTSAGVYFKAGGPITYKVMREVKALAYFVNGTAQDVILCDGSPRGLLACQYNTGNFSDGFYPFTNSSLVKQKFIVYRENSVNTTCTLHNFIFHNETGANPNPSGVQNIQTYQTKTAQSGYYNFNFSFLSSFVYKESNFMYGSYHPSCKFRLETINNGLWFNSLSVSIAYGPLQGGCKQSVFKGRATCCYAYSYGGPSLCKGVYSGELDHNFECGLLVYVTKSGGSRIQTATEPPVITQNNYNNITLNTCVDYNIYGRTGQGFITNVTDSAVSYNYLADAGLAILDTSGSIDIFVVQGEYGLNYYKVNPCEDVNQQFVVSGGKLVGILTSRNETGSQLLENQFYIKITNGTRRFRRSITENVANCPYVSYGKFCIKPDGSIATIVPKQLEQFVAPLFNVTENVLIPNSFNLTVTDEYIQTRMDKVQINCLQYVCGSSLDCRKLFQQYGPVCDNILSVVNSVGQKEDMELLNFYSSTKPAGFNTPVLSNVSTGEFNISLLLTNPSSRRKRSLIEDLLFTSVESVGLPTNDAYKNCTAGPLGFFKDLACAREYNGLLVLPPIITAEMQALYTSSLVASMAFGGITAAGAIPFATQLQARINHLGITQSLLLKNQEKIAASFNKAIGHMQEGFRSTSLALQQIQDVVSKQSAILTETMASLNKNFGAISSVIQEIYQQFDAIQANAQVDRLITGRLSSLSVLASAKQAEYIRVSQQRELATQKINECVKSQSIRYSFCGNGRHVLTIPQNAPNGIVFIHFSYTPDSFVNVTAIVGFCVKPANASQYAIVPANGRGIFIQVNGSYYITARDMYMPRAITAGDVVTLTSCQANYVSVNKTVITTFVDNDDFDFNDELSKWWNDTKHELPDFDKFNYTVPILDIDSEIDRIQGVIQGLNDSLIDLEKLSILKTYIKWPWYVWLAIAFATIIFILILGWVFFMTGCCGCCCGCFGIMPLMSKCGKKSSYYTTFDNDVVTEQYRPKKSV

Function

Spike protein S1: attaches the virion to the host cell membrane by interacting with sialic acids, initiating the infection.
Spike protein S2': Acts as a viral fusion peptide after S2 cleavage occurring upon virus endocytosis.
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.
attaches the virion to the host cell membrane by interacting with sialic acids, initiating the infection.
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.
Acts as a viral fusion peptide after S2 cleavage occurring upon virus endocytosis.

Subunit

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

Similarity

Belongs to the gammacoronaviruses spike protein family.

Keywords

Cleavage on pair of basic residues   Coiled coil   Fusion of virus membrane with host endosomal membrane   Fusion of virus membrane with host membrane   Glycoprotein   Host membrane   Host-virus interaction   Membrane   Reference proteome   Signal   Transmembrane   Transmembrane helix   Viral attachment to host cell   Viral envelope protein   Viral penetration into host cytoplasm   Virion   Virulence   Virus endocytosis by host   Virus entry into host cell  

Feature

chain  Spike protein S1

Uniprot

Q778S6   P11223   Q0PIM4   Q0Z8B1   Q91QT1   F4MIY6   + More
Q4ZJU3   Q5MNZ2   Q4ZJU6   Q4ZJS3   Q4ZJS2   Q4ZJU5   Q4ZJU4   Q4ZJU2   A0A346M357   A0A0M3R808   A0A4Y5SXZ2   A0A1X9Y2W0   A0A1W6AWJ3   A0A023PP15   A0A1V0QHB0   A0A023PNG1   A0A023PMY1   A0A4Y5SY76   A0A218MNH9   A0A023PN26   A0A4Y5SZ29   U3N710   A0A023PNV3   A0A023PLR7   C7S7Y0   G4XMR7   G3C7B9   A0A023PLW4   A0A023PMV0   Q5EMM1   A0A023PNA4   B7SXS2   A0A023PP42   K9LVN4   A0A023PMN7   A0A023PLZ1   A0A023PN03   A0A023PNR0   A0A023PMI1   A0A4V6MB96   C3VPK3   A0A023PP70   A0A023PND9   A0A023PNN6   A0A023PMR7   A0A023PM26   G4RJ60   A0A023PNY4   C1KAB1   A0A023PNA6   A0A023PNS5   G4RJ62   Q98Y27   G4XMQ7   E5D0C2   A0A023PML1   A0A3S9IHQ0   P12651   E5D0B1   A0A023PN76   Q66VA7   F4MIX6   A0A4Y5SXR7   Q5XLA4   C7S859   G4RJ61   G4RJ68   A0A3S9IHM9   A0A516UWA4   Q66178   A0A4D6NY48   A0A4Y5SXY5   F4MIW6   C6K2F8   G4RJ66   F4MIZ6   G4RJ63   G4RJ70   G8FQ94   G8FQ95   G4RJ67   G4RJ64   A0A023PNM3   G8FQ93   G4RJ65   G0ZGK1   F4MIP6   G8FQ91   G8FQ90   P12650   G8FQ89   G8FQ96   G8FQA7   A0A0K1RMX2  

Pubmed

11711626    2984314    3025348    16137658    15140989    16537586    + More
19553314    24314633    29035787    17461266    21539870    15661153    28495648    26482289    28646651    25311758    23178317    21994806    16990149    19100792    20652731    21909766    30526618    2429473    16934878    15722532    29684066    22005179    2841803   

EMBL

AJ311317    CAC39114.1    M95169    X02342    DQ001342    DQ001339    + More
DQ830981    ABH01142.1    DQ664534    ABG48666.1    AJ311362    CAC39300.1    FJ904722    ADA83557.1    DQ001337    AAY21245.1    AY692454    AAV98206.1    DQ001334    AAY21242.1    DQ001340    AAY21246.1    DQ001341    AAY21247.1    DQ001335    AAY21243.1    DQ001336    AAY21244.1    DQ001338    AAY24423.1    MG913343    AXQ05201.1    KP868573    ALC78747.1    MK937833    QDA76336.1    KY805845    ARS23139.1    KY626045    ARJ35791.1    KJ425505    AHX26073.1    KY588135    ARE67884.1    KJ425491    KJ425499    KJ425512    AHX25947.1    AHX26019.1    AHX26136.1    KJ435283    AHX26145.1    MK937831    QDA76318.1    KY273667    ASF20080.1    KJ425494    AHX25974.1    MK937832    QDA76327.1    KF188436    AGW24533.1    KJ425495    AHX25983.1    KJ425487    AHX25911.1    EU714028    ACH72794.1    JF828981    KJ425501    KJ425507    MG763935    MK937829    AEP84746.1    AHX26037.1    AHX26091.1    AVX27612.1    QDA76300.1    GU393335    ADV71785.1    KJ425492    AHX25956.1    KJ425508    AHX26100.1    AY856348    AAW83034.1    KJ425509    AHX26109.1    EU822341    JF330899    ACJ50199.1    ADY62552.1    KJ425510    AHX26118.1    JQ920397    AFP50274.1    KJ425498    AHX26010.1    KJ425497    AHX26001.1    KJ425489    AHX25929.1    KJ425511    AHX26127.1    KJ425488    AHX25920.1    MK071267    QCS40640.1    FJ888351    KT203557    ACQ55230.1    ALE71331.1    KJ435285    KT736031    AHX26163.1    AMK51938.1    KJ435284    AHX26154.1    KJ425506    AHX26082.1    KJ425503    AHX26055.1    KJ425502    AHX26046.1    FJ829873    ACX71842.1    KJ425500    AHX26028.1    FJ807652    ACO37566.1    KJ425486    AHX25902.1    KJ425490    AHX25938.1    FJ829875    ACX71844.1    AF352315    AAK27168.1    JF828980    KJ435286    AEP84736.1    AHX26172.1    GQ504725    ADP06515.1    KJ425493    AHX25965.1    MH539771    AZP23930.1    M21883    DQ834384    AY851295    DQ830980    GQ504724    ADP06504.1    KJ425504    AHX26064.1    AY702085    AAU09490.1    FJ904721    ADA83547.1    MK937828    QDA76291.1    AY761141    AAV28722.1    EU817497    ACJ12834.1    FJ829874    ACX71843.1    FJ829881    ACX71850.1    MH539772    AZP23949.1    MK581200    MK581201    QDQ69095.1    QDQ69108.1    X04722    CAA28431.1    MK728875    QCE31533.1    MK937830    QDA76309.1    FJ904720    ADA83537.1    GQ149080    ACS34957.1    FJ829879    ACX71848.1    FJ904723    ADA83567.1    FJ829876    ACX71845.1    FJ829883    ACX71852.1    JN022541    AER08726.1    JN022542    AER08727.1    FJ829880    ACX71849.1    FJ829877    ACX71846.1    KJ425485    AHX25893.1    JN022540    AER08725.1    FJ829878    ACX71847.1    JF274479    AEL12221.1    FJ904713    ADA83467.1    JN022538    AER08723.1    JN022537    AER08722.1    M21515    JN022536    AER08721.1    JN022543    AER08728.1    JN022554    AER08739.1    KR902510    AKV63205.1   

Proteomes

UP000114388    UP000006717    UP000101586    UP000107149    UP000180341    UP000149006    + More
UP000118008    UP000159206    UP000163887    UP000166253    UP000102797    UP000170189    UP000173109    UP000146865    UP000165788    UP000097868    UP000113245    UP000167410    UP000136241    UP000173215    UP000155946    UP000102163    UP000103149    UP000138146    UP000113896    UP000170844    UP000122234    UP000155572    UP000106511    UP000132365    UP000180343    UP000107224    UP000174151    UP000136440    UP000149404    UP000158124    UP000158949    UP000113939    UP000108224    UP000102121    UP000120642    UP000149491    UP000161686    UP000114242    UP000120286    UP000007642    UP000096468    UP000107291    UP000117985    UP000169726    UP000107830    UP000165485    UP000098752    UP000167075    UP000159542    UP000145806    UP000151562   

PRIDE

P11223   

Pfam

PF01600   Corona_S1
PF01601   Corona_S2

Interpro

IPR002552   Corona_S2
IPR042549   GAMMA_CORONA_SPIKE
IPR027400   S_HR2
IPR002551   Corona_S1

Gene 3D

1.20.5.790    

ProteinModelPortal

Q778S6   P11223   Q0PIM4   Q0Z8B1   Q91QT1   F4MIY6   + More
Q4ZJU3   Q5MNZ2   Q4ZJU6   Q4ZJS3   Q4ZJS2   Q4ZJU5   Q4ZJU4   Q4ZJU2   A0A346M357   A0A0M3R808   A0A4Y5SXZ2   A0A1X9Y2W0   A0A1W6AWJ3   A0A023PP15   A0A1V0QHB0   A0A023PNG1   A0A023PMY1   A0A4Y5SY76   A0A218MNH9   A0A023PN26   A0A4Y5SZ29   U3N710   A0A023PNV3   A0A023PLR7   C7S7Y0   G4XMR7   G3C7B9   A0A023PLW4   A0A023PMV0   Q5EMM1   A0A023PNA4   B7SXS2   A0A023PP42   K9LVN4   A0A023PMN7   A0A023PLZ1   A0A023PN03   A0A023PNR0   A0A023PMI1   A0A4V6MB96   C3VPK3   A0A023PP70   A0A023PND9   A0A023PNN6   A0A023PMR7   A0A023PM26   G4RJ60   A0A023PNY4   C1KAB1   A0A023PNA6   A0A023PNS5   G4RJ62   Q98Y27   G4XMQ7   E5D0C2   A0A023PML1   A0A3S9IHQ0   P12651   E5D0B1   A0A023PN76   Q66VA7   F4MIX6   A0A4Y5SXR7   Q5XLA4   C7S859   G4RJ61   G4RJ68   A0A3S9IHM9   A0A516UWA4   Q66178   A0A4D6NY48   A0A4Y5SXY5   F4MIW6   C6K2F8   G4RJ66   F4MIZ6   G4RJ63   G4RJ70   G8FQ94   G8FQ95   G4RJ67   G4RJ64   A0A023PNM3   G8FQ93   G4RJ65   G0ZGK1   F4MIP6   G8FQ91   G8FQ90   P12650   G8FQ89   G8FQ96   G8FQA7   A0A0K1RMX2  

PDB

6CV0     E-value=0,     Score=5063