Strain

CHINA_AVIAN_2008_NC_016995 (Region: China: Hong Kong;  Strain: Wigeon coronavirus HKU20, complete genome.;  Date: 2008)

Gene

spike glycoprotein

Description

Annotated in NCBI,  spike glycoprotein

Location

NC_016995(+):18817-22455

GenBank Accession

YP_005352871.1

Full name

Spike glycoprotein      

Alternative Name

E2
Peplomer protein

CDS

ATGTACAGGTTTGCTATACTAATGTTGGTCATTTCGCCAACCCTAGCTGCATCCATAGCTGATAAAGTTTTGGATGTAGTAACCTTTCCCGGAGCATCTCGGTTGTTGTACCCACAACACTACCAACAACCCCAAGTAAGGGGGTGGACTGATGATATTGGTGTTGATGGTCGCATACCTGCAACCTATCCACTAACCAACACCTTCTATCTTTCAAATACCACCACACCAGTTGATGGTGTTTATACTAGTCTTCAGCCCTTATTAATTCGTTGTAAGTTTAAATACGTCAATGATACTGTCAATGCTGGTAAAATTCTTACTATGTATTTTAACCTCACCAATAACACAGGTAGATGTGACGGGAATTCGGAAAAGGTTGGTCTTGTGGATGCCATCAGGTTTCAAATTAATGTCACAACCGACATATTACAGCTCACTGCAGGCAGTATTAACTTTACTACACCGGACGGAGAGCTGTATACATTACATTGTCTTAACACGACACTTGGTGTAGGCCAGGATTATTACCCATCTCAAAGCCGCACGCGGCAGTCTGGTGTTACCTATCATTGTTATATGATATATCGTAACACATCCTACGCCTACAGCGCTAATGAATACACTTATCGTGTGCTTCAATATTTGGGTCCCTTACCAGCATCAGTTAGGGAAATTGTTGCTTTTAGTAATGGATTCATTTACATTAATGGCATTCTTCTTTCGCGAATACCCGCGTTGCATAAAGTTGATTTTGGTCTTGTTAAGAGTGCCCATACGTCAGATTATTATGTTATCTTGTTTGCTGATATGGTTGACGTAATGGTCAACATATCCGCCACTGAAATGCAGTCTATCTTTTACTGCATAACCCCTTTTGAGCAGGTTAAATGTTCACAGAAACAAACCACTCTTTCTGATGGGTTCTATTCCACATCTGCCATTGAAGTCCTACAGCGCCAGCGCACATTTGTAGGGTTACCGATGGCTATTAACATTACTACGCTTAATTTTGCTATTAGTTATTTGAATACCAAGGCTAATCCTAGTTTAGGTGCACCACAGGAAGTCAATCTTACCATAAATGGGTTTGCAGATCAATTCTGTGTTACAACCTCCCAGTTTATGGTTACTCTTAATGTGACCTGTCTCGTTCATAATAATACTAGTATAATACCCTGTCCACAGGCTTACACGGCAGAAATCTCACCGGGGGATTGCCCATTTAATTTTTTGGATGTTAATAACTATTTAATGTTTGACAGCATTTGCTTTTCACCTTCTCCCAGTGGTGACAGCTGTCAGATGGTTATTAATAAAGTCTGGGCCAATAATCGCATACCTATGAGTAGCGTTTATGTCTCCTATGTCTATGGCAACCAGATAGTCGGTGTACCTCGACACGATCTCGTGCAGTTGGATCATGTCGTGTTTAATTTGTGCACAGACTACACCATTTATGGGTATACCGGTACTGGTGTTATACGTGAAACTAACACCACATACTTTGCCGGTTATGCCTATGCATCACCAGCTGGTCAACTCGTTGCCTATAAAAATCTTACTACTGGTGCTATTAATTCTATAACACCATGTAAGTTTAGTCAACAATTAGCCGTGTATAATGATACACCTGTAGCCCTTGTGTCAGCGGTGCCCTCGCAGGACTTTGGGTTTACCAATGCAACCTCTATGGGTACCTTTGTTGTCAATTCAAATGCAACTAATTGCACCATTCCAGCTCTTACTTATGGCCCACTTGGCATTTGTGCCAATGGCGCTCCATATGTAGTACCTACAGGTGAAGGCCAAGAACCTAGTGTTGTCCCCATTTCTACGGGCAACATTTCAATACCTGTCAATTTTACTGTAGCCATACAGCCTGAGTATCTACAGGTTTATACTGAGCAGGTTGTTGTAGACTGTGCCACTTATGTTTGCAACGGTAACCCATTGTGTAACAAGTTGTTGTTACAATACACTTCAGCTTGCGACACAATTGAGCAGGCGTTGCAAATGAGCGCCCGTTTAGAGTCTAGTGAAGTCTCTAACATGCTACACATTTCAACGCAGGCTCTGGATTTGGCTAACATCTCAAATTTTGAGGGTTATAATATGTCCTTTGTTTTGCCTGCTGTTAAACAGGGTAGGTCTGCCTTAGAAGACTTGCTATTTACTAAAGTAGTTACAGCTGGACTGGGCACAGTAGATGCTGACTATGAGAAATGTGCTAAAGGCATGGACATAGCAGACCTTGTATGTGTCCAGTACTATAACGGTATCATGGTGCTCCCCGGCGTAGCAAATGCTGGCAAAATGGCTGAGTACACAGCATCCCTTACTGGCGGTATGGTTATGGGTGGTATTACATCAGCAGCCTCTATACCATTTTCCTTAGCGGTACAAAGCCGCCTTAATTATGTAGCTCTGCAAACAGGTGTTATGTTAGATAATCAGAAGCTTCTAGCAGATTCCTTTAATAAGGCTATGGAGACAATTTCTGGTGCATTTAATTCACTTAATTCTGCTGTGCATGAAACTATTAATGTTGTTAACACTCTATCATCTGCACTTACTAAGATACAGAGTGTTGTCAATCAGCATACTACAGCCTTAAATCAGCTAACTCAGCAGTTGGCTAATAATTTCCAGGCTATATCTTCGTCTATTACAGACATTTATAACAGGTTGGGTCAACTAGAGGCTGATGCTCAGGTAGATCGGCTTATTACAGGTCGGTTGGCAGCCCTCAATGCATTTGTGTCCCAAACCTTAACCAAGGCAGAGCAGGTCCGCCAATCTAGGTTGCTTGCTCAGCAGAAAGTTAATGAGTGTGTCAAATCGCAGTCTCAGCGGTTTGGTTTCTGTGGCAATGGTTCTCACATCTTTACTATTGCCAATGCCGCGCCTGATGGCATTATGTTTTTGCACACGGTACTACAACCTGTAAGCTACATTACTGTTGTAGCCTATTCAGGGCTGTGTGTAGACAACACTTATGGCTACGCTCTTAAAGAGCCTAACCTAGCACTTGTGCAGTATAATGGTTATTATGTTACTCCGCGTAATATGTATCAACCACGTCCAGCTACTACAGCTGACTTTGTGCAAATACAATCTTGTGATGTTACCCTCTATAACATTACTTACAATAATATATCTTTGGTCATACCAGACTTTGTGGATACCAACAAAACTATTGAAGATATCATTTCTTCAATACCTAATAATACTGCGCCTAGTTTAGAAATAGCCAGTCTTAATCTGACTGTACTAAACCTGACGTCAGAGCTAGAACAATTAAAAGCCTCCACTGGCAATTTTACTCAAATTTCTCAGGAAATACAGGATTACATAAATAAACTCAATGACACTCTAGTTGACTTAGAGTGGCTCAACAGAGTAGAAACTTATGTTAAATGGCCATGGTGGGTGTGGCTTCTTATCTTTTTAGCCATTTGTACTTTTATAATAATTGTCGTAACAATCTTCCTATGCACAGGTTGCTGTGGTGGATGTTTTGGCTGTTTTGGTGGGTGCTGTGGTTTGTTTAGCAGAGTTAAACACCATGAGTTTTCGCACTTACCTGTAGAAGAACAAGATGGCTCAATACCAATTACCTATAAGAAAGTTAATTAA

Protein

MYRFAILMLVISPTLAASIADKVLDVVTFPGASRLLYPQHYQQPQVRGWTDDIGVDGRIPATYPLTNTFYLSNTTTPVDGVYTSLQPLLIRCKFKYVNDTVNAGKILTMYFNLTNNTGRCDGNSEKVGLVDAIRFQINVTTDILQLTAGSINFTTPDGELYTLHCLNTTLGVGQDYYPSQSRTRQSGVTYHCYMIYRNTSYAYSANEYTYRVLQYLGPLPASVREIVAFSNGFIYINGILLSRIPALHKVDFGLVKSAHTSDYYVILFADMVDVMVNISATEMQSIFYCITPFEQVKCSQKQTTLSDGFYSTSAIEVLQRQRTFVGLPMAINITTLNFAISYLNTKANPSLGAPQEVNLTINGFADQFCVTTSQFMVTLNVTCLVHNNTSIIPCPQAYTAEISPGDCPFNFLDVNNYLMFDSICFSPSPSGDSCQMVINKVWANNRIPMSSVYVSYVYGNQIVGVPRHDLVQLDHVVFNLCTDYTIYGYTGTGVIRETNTTYFAGYAYASPAGQLVAYKNLTTGAINSITPCKFSQQLAVYNDTPVALVSAVPSQDFGFTNATSMGTFVVNSNATNCTIPALTYGPLGICANGAPYVVPTGEGQEPSVVPISTGNISIPVNFTVAIQPEYLQVYTEQVVVDCATYVCNGNPLCNKLLLQYTSACDTIEQALQMSARLESSEVSNMLHISTQALDLANISNFEGYNMSFVLPAVKQGRSALEDLLFTKVVTAGLGTVDADYEKCAKGMDIADLVCVQYYNGIMVLPGVANAGKMAEYTASLTGGMVMGGITSAASIPFSLAVQSRLNYVALQTGVMLDNQKLLADSFNKAMETISGAFNSLNSAVHETINVVNTLSSALTKIQSVVNQHTTALNQLTQQLANNFQAISSSITDIYNRLGQLEADAQVDRLITGRLAALNAFVSQTLTKAEQVRQSRLLAQQKVNECVKSQSQRFGFCGNGSHIFTIANAAPDGIMFLHTVLQPVSYITVVAYSGLCVDNTYGYALKEPNLALVQYNGYYVTPRNMYQPRPATTADFVQIQSCDVTLYNITYNNISLVIPDFVDTNKTIEDIISSIPNNTAPSLEIASLNLTVLNLTSELEQLKASTGNFTQISQEIQDYINKLNDTLVDLEWLNRVETYVKWPWWVWLLIFLAICTFIIIVVTIFLCTGCCGGCFGCFGGCCGLFSRVKHHEFSHLPVEEQDGSIPITYKKVN

Function

S1 region attaches the virion to the cell membrane by interacting with host ANPEP/aminopeptidase N, initiating the infection. Binding to the receptor probably induces conformational changes in the S glycoprotein unmasking the fusion peptide of S2 region and activating membranes fusion. S2 region belongs to the 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) regions 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.

Subunit

Homotrimer. During virus morphogenesis, found in a complex with M and HE proteins. Interacts with host ANPEP.

Similarity

Belongs to the alphacoronaviruses spike protein family.

Keywords

3D-structure   Coiled coil   Glycoprotein   Host membrane   Host-virus interaction   Membrane   Signal   Transmembrane   Transmembrane helix   Viral attachment to host cell   Viral envelope protein   Virion   Virulence   Virus entry into host cell   Reference proteome  

Feature

chain  Spike glycoprotein

Uniprot

H9BR25   A0A2U9I6C2   A0A482JX42   A0A482JZV2   A0A0U1UZ37   H9BR08   + More
A0A1L2KGE4   A4ULL1   A0A0U1WJW2   A0A2Z5XXT6   A0A2Z5XXS4   A0A1L2KGB2   H9BR00   F1DB14   A0A1L2KGF1   A0A2Z5XXR5   A0A0P0KBC5   A0A0P0K0X5   A0A0N7J128   A0A0P0KXK6   A0A5B9BH95   A0A0P0G321   K4P2Y7   Q6Q1S2   A0A384RHS8   A0A384QZE9   A0A5B9BIJ4   A0A5B9MUE4   I7CMD1   A0A384RHT2   A0A384QXZ7   A0A1V0PKX8   A0A1V0E0U5   H9EJ44   A0A0K1D6F6   A0A1V0E0W0   H9EJV2   A0A0P0KR98   U3M7G5   Q06Y16   A0A384RBV6   A0A5B9BH24   A0A1L2YVI8   A0A2U8JDM5   H9EJ93   A0A384RK30   U3M6U5   H9EJA0   H9EJ51   U3M6Q4   H9EJ72   H9EJW4   A0A1V0PKW6   H9EJ86   A0A1V0PKX1   A0A0U2GNG3   A0A384R2Q9   U3M7H2   A0A513ZT30   A0A2H4ZBM8   U3M6S0   H9EJ37   A0A2L0WQE1   A0A0U2GQI5   A0A0U2GQ76   A0A0U2GMQ4   A0A0U2GRB2   A0A1C8YZ34   A0A0U2GN50   A0A0U2GRL6   A0A1B3TNA4   A0A0U2GMN8   A0A4Y5QL66   A0A1C8YZ37   A0A5B9BHU7   I1VWF5   H9EJ16   A0A1Y0EV12   A0A1C8YZ26   Q06Y10   A0A2H4ZBN0   A0A0U2GME6   P15423   A0A0U2GN82   A0A0U2GMG2   A0A0P0KI80   A0A059SGA9   Q1HVM6   H1AG29   A0A0N7J129   A0A5B9MSJ9   A0A0P0K6L9   A0A0P0KR90   A0A5B9BGI8   A0A0P0KMM1   Q1HVL3   Q1HVL0   S5YGU2   Q1HVL4   S5YAI3  

Pubmed

22278237    29875375    17267506    19239771    22561208    26378164    + More
27799635    15034574    15073334    15897467    22879617    29741740    22837419    17054987    26678874    29166910    27528677    31067830    2345367    11369870    9870593    2701946    1350662    8970993    12551991    12634402    11162792    16603522    22673931   

EMBL

JQ065048    AFD29234.1    MH013337    AWR88316.1    MG916902    QBP43268.1    + More
MG916903    QBP43279.1    KJ473810    AIA62271.1    JQ065046    AFD29217.1    KY073747    APD51499.1    EF434381    ABO88151.1    KJ473807    AIA62252.1    LC364344    BBC54842.1    LC364343    BBC54832.1    KY073744    APD51475.1    JQ065045    AFD29209.1    HQ728485    ADX59488.1    KY073748    APD51507.1    LC364342    BBC54822.1    KT253267    ALK28773.1    KT253265    ALK28771.1    KT253261    KT253263    ALK28767.1    ALK28769.1    KT253262    ALK28768.1    MK334044    QED88019.1    KT381875    KU521535    ALJ53431.1    ANU06084.1    JX504050    AFV53148.1    AY567487    AY518894    AY758297    AY758298    AY758300    AY758301    KM055634    AIW52831.1    KM055642    AIW52839.1    MK334043    QED88012.1    MN306040    QEG03748.1    JX104161    JX524171    KM055632    KM055633    KM055635    KM055636    KM055637    KM055648    KM055649    KM055650    MG428699    MG428700    MG428701    MG428702    MG428703    MG428704    MG428705    MG428706    AFO70497.1    AFQ55884.1    AIW52829.1    AIW52830.1    AIW52832.1    AIW52833.1    AIW52834.1    AIW52845.1    AIW52846.1    AIW52847.1    AWK59931.1    AWK59937.1    AWK59943.1    AWK59949.1    AWK59955.1    AWK59961.1    AWK59967.1    AWK59973.1    KM055644    AIW52841.1    KM055639    KM055640    KM055641    KM055645    KM055647    AIW52836.1    AIW52837.1    AIW52838.1    AIW52842.1    AIW52844.1    KY554970    ARE29979.1    KY674916    ARB07406.1    JQ765567    AFD98778.1    KT266906    KX179494    KX179495    KX179496    AKT07952.1    APF29061.1    APF29062.1    APF29063.1    KY674915    KY554967    ARB07399.1    ARE29961.1    JQ771055    JQ771057    JQ771058    AFD64748.1    AFD64754.1    AFD64757.1    KT253270    ALK28781.1    KF530107    AGT51345.1    DQ445911    ABE97137.1    KM055638    AIW52835.1    MK334045    QED88026.1    KX179500    APF29071.1    MG428707    AWK59979.1    JQ765574    AFD98827.1    KM055643    AIW52840.1    KF530104    KF530106    KF530108    KF530109    KF530111    KF530113    KF530114    AGT51324.1    AGT51338.1    AGT51352.1    AGT51359.1    AGT51373.1    AGT51387.1    AGT51394.1    JQ765575    AFD98834.1    JQ765568    AFD98785.1    KF530105    AGT51331.1    JQ765571    JQ765572    AFD98806.1    AFD98813.1    JQ771059    AFD64760.1    KY554968    ARE29967.1    JQ765573    AFD98820.1    KY554969    KY554971    KY829118    ARE29973.1    ARE29985.1    ARK08627.1    KT368916    ALA50256.1    KM055646    AIW52843.1    KF530112    AGT51380.1    MN026166    QDH43736.1    MF996621    MF996622    AUF73167.1    KF530110    AGT51366.1    JQ765566    AFD98771.1    MG772808    AVA26873.1    KT368915    ALA50249.1    KT368899    ALA50137.1    KT368901    ALA50151.1    KT368907    KT368908    ALA50193.1    ALA50200.1    KT253327    AOI28283.1    KT368898    ALA50130.1    KT368903    ALA50165.1    KU291449    AOG74789.1    KT368892    KT368893    KT368894    KT368902    KT368904    KT368905    KT368906    KT368909    KT368910    KT368911    KT368912    KT368913    KT368914    ALA50088.1    ALA50095.1    ALA50102.1    ALA50158.1    ALA50172.1    ALA50179.1    ALA50186.1    ALA50207.1    ALA50214.1    ALA50221.1    ALA50228.1    ALA50235.1    ALA50242.1    MK720945    MK720946    QCX35167.1    QCX35178.1    KT253324    KT253326    KT253328    AOI28259.1    AOI28275.1    AOI28291.1    MK334046    QED88033.1    JQ410000    AFI49431.1    JQ765563    AFD98750.1    KY983586    ARU07594.1    KT253325    AOI28267.1    DQ445912    JQ771056    JQ771060    JQ765564    JQ765565    JQ765569    JQ765570    ABE97130.1    AFD64751.1    AFD64763.1    AFD98757.1    AFD98764.1    AFD98792.1    AFD98799.1    MF996623    AUF73168.1    KT368895    KT368896    MF593473    ALA50109.1    ALA50116.1    ATI09437.1    X16816    AF304460    AF344186    AF344187    AF344188    AF344189    Y09923    Y10051    Y10052    X15654    KT368900    ALA50144.1    KT368897    ALA50123.1    KT253266    ALK28772.1    KF293664    KF293665    KF293666    AGW80948.1    DQ243963    ABB90506.1    AB691763    BAL45637.1    KT253269    ALK28775.1    MN306018    QEG03731.1    KT253271    ALK28787.1    KT253264    ALK28770.1    MK334047    QED88040.1    KT253268    ALK28774.1    DQ243976    ABB90519.1    DQ243979    ABB90522.1    KF514432    AGT21360.1    DQ243973    DQ243974    DQ243975    ABB90516.1    ABB90517.1    ABB90518.1    KF514433    AGT21367.1   

Proteomes

UP000167590    UP000144177    UP000162232    UP000106394    UP000204102    UP000142997    + More
UP000145724    UP000103541    UP000008573    UP000161757    UP000098690    UP000158277    UP000125140    UP000141634    UP000122373    UP000174240    UP000115484    UP000129674    UP000106901    UP000140530    UP000144638    UP000146557    UP000153644    UP000162862    UP000167796    UP000110792    UP000168590    UP000171901    UP000134798    UP000141321    UP000100468    UP000152663    UP000136929    UP000243277    UP000143818    UP000108941    UP000153625    UP000136947    UP000173458    UP000120649    UP000151210    UP000116691    UP000103783    UP000100137    UP000103248    UP000108758    UP000110675    UP000115199    UP000115399    UP000124352    UP000128900    UP000136940    UP000152773    UP000153580    UP000171347    UP000173795    UP000146121    UP000173136    UP000105969    UP000130385    UP000138462    UP000151180    UP000151840    UP000101679    UP000169049    UP000006716    UP000104585    UP000147133    UP000118770    UP000096398    UP000110267    UP000139984   

PRIDE

P15423   

Pfam

PF01600   Corona_S1
PF01601   Corona_S2

Interpro

IPR002551   Corona_S1
IPR002552   Corona_S2
IPR042552   ALPHA_CORONA_SPIKE

ProteinModelPortal

H9BR25   A0A2U9I6C2   A0A482JX42   A0A482JZV2   A0A0U1UZ37   H9BR08   + More
A0A1L2KGE4   A4ULL1   A0A0U1WJW2   A0A2Z5XXT6   A0A2Z5XXS4   A0A1L2KGB2   H9BR00   F1DB14   A0A1L2KGF1   A0A2Z5XXR5   A0A0P0KBC5   A0A0P0K0X5   A0A0N7J128   A0A0P0KXK6   A0A5B9BH95   A0A0P0G321   K4P2Y7   Q6Q1S2   A0A384RHS8   A0A384QZE9   A0A5B9BIJ4   A0A5B9MUE4   I7CMD1   A0A384RHT2   A0A384QXZ7   A0A1V0PKX8   A0A1V0E0U5   H9EJ44   A0A0K1D6F6   A0A1V0E0W0   H9EJV2   A0A0P0KR98   U3M7G5   Q06Y16   A0A384RBV6   A0A5B9BH24   A0A1L2YVI8   A0A2U8JDM5   H9EJ93   A0A384RK30   U3M6U5   H9EJA0   H9EJ51   U3M6Q4   H9EJ72   H9EJW4   A0A1V0PKW6   H9EJ86   A0A1V0PKX1   A0A0U2GNG3   A0A384R2Q9   U3M7H2   A0A513ZT30   A0A2H4ZBM8   U3M6S0   H9EJ37   A0A2L0WQE1   A0A0U2GQI5   A0A0U2GQ76   A0A0U2GMQ4   A0A0U2GRB2   A0A1C8YZ34   A0A0U2GN50   A0A0U2GRL6   A0A1B3TNA4   A0A0U2GMN8   A0A4Y5QL66   A0A1C8YZ37   A0A5B9BHU7   I1VWF5   H9EJ16   A0A1Y0EV12   A0A1C8YZ26   Q06Y10   A0A2H4ZBN0   A0A0U2GME6   P15423   A0A0U2GN82   A0A0U2GMG2   A0A0P0KI80   A0A059SGA9   Q1HVM6   H1AG29   A0A0N7J129   A0A5B9MSJ9   A0A0P0K6L9   A0A0P0KR90   A0A5B9BGI8   A0A0P0KMM1   Q1HVL3   Q1HVL0   S5YGU2   Q1HVL4   S5YAI3  

PDB

5SZS     E-value=0,     Score=2217