Strain

CHINA_HS_2004_NC_006577 (Region: China: Hong Kong;  Strain: Human coronavirus HKU1, complete genome.;  Date: 2004)

Gene

spike glycoprotein

Description

Annotated in NCBI,  spike glycoprotein

Location

NC_006577(+):22942-27012

GenBank Accession

YP_173238.1

Full name

Spike glycoprotein      

Alternative Name

E2
Peplomer protein

CDS

ATGTTATTAATTATTTTTATTTTGCCTACAACATTAGCTGTTATAGGTGATTTTAATTGTACTAATTTTGCTATTAATGATTTAAACACCACAGTTCCTCGCATAAGTGAGTATGTTGTGGATGTTTCTTATGGTTTGGGTACATATTATATACTTGATCGTGTTTATTTAAATACTACTATATTATTTACTGGTTATTTCCCTAAATCTGGTGCCAATTTTAGGGATCTATCTTTAAAAGGTACTACATATTTGAGTACTCTTTGGTATCAGAAACCCTTTTTATCTGATTTTAATAATGGTATTTTTTCTAGAGTTAAGAATACTAAGTTGTATGTTAATAAAACTTTGTATAGTGAGTTTAGTACTATAGTTATAGGTAGTGTTTTTATTAACAACTCTTATACTATTGTTGTTCAACCTCATAATGGTGTTTTGGAGATTACAGCTTGTCAATACACTATGTGTGAGTATCCTCATACTATTTGTAAATCTAAAGGTAGTTCTCGTAATGAATCTTGGCATTTTGATAAATCTGAACCTTTGTGTCTGTTCAAGAAAAATTTTACTTATAATGTTTCTACAGATTGGTTGTATTTTCATTTTTATCAAGAACGTGGCACTTTTTATGCTTATTATGCTGATTCTGGCATGCCTACTACTTTTTTATTTAGTTTGTATCTTGGTACTCTTTTATCTCATTATTATGTTTTGCCTTTGACTTGTAATGCTATATCTTCTAATACTGATAATGAGACTTTACAATATTGGGTCACACCTTTGTCTAAACGCCAATATCTTCTTAAATTTGACAACCGTGGTGTTATTACTAATGCTGTTGATTGTTCTAGTAGTTTCTTTAGCGAGATTCAATGTAAAACTAAATCTTTATTACCTAATACTGGTGTTTATGACTTATCTGGTTTTACTGTTAAGCCTGTTGCAACTGTACATCGTCGTATTCCTGATTTACCTGATTGTGACATTGATAAATGGCTTAACAATTTTAATGTACCCTCACCTCTTAATTGGGAACGTAAAATTTTTTCTAATTGCAACTTTAATTTGAGTACTTTGCTTCGTTTAGTTCATACTGATTCTTTTTCTTGTAATAATTTTGATGAATCTAAGATATATGGTAGTTGTTTTAAGAGTATTGTTTTAGATAAATTTGCCATACCCAACTCCAGACGATCTGATTTGCAGTTGGGCAGTTCTGGTTTTCTGCAATCTTCTAATTATAAAATTGACACTACTTCTAGTTCTTGTCAATTGTATTATAGTTTGCCTGCAATTAATGTTACTATTAATAATTATAATCCTTCTTCTTGGAATAGAAGGTATGGTTTTAATAATTTTAATTTGAGCTCTCATAGTGTTGTTTACTCACGTTATTGTTTTTCTGTTAATAATACTTTTTGTCCTTGTGCTAAACCTTCTTTTGCTTCAAGTTGCAAGAGTCATAAACCACCTTCTGCTTCCTGTCCTATTGGTACTAATTATCGTTCTTGTGAGAGTACTACTGTACTCGACCACACTGACTGGTGTAGGTGTTCTTGTTTACCTGATCCTATAACTGCTTATGACCCTAGGTCTTGTTCTCAAAAAAAGTCTCTGGTTGGTGTTGGTGAACATTGTGCAGGGTTCGGTGTTGATGAAGAAAAGTGTGGTGTATTGGATGGATCATATAATGTTTCTTGTCTTTGTAGTACTGATGCCTTTCTAGGTTGGTCTTATGACACTTGCGTCAGTAACAACCGTTGTAATATTTTTTCTAATTTTATTTTAAATGGTATCAATAGTGGTACCACTTGTTCTAATGATTTATTGCAGCCTAATACTGAAGTTTTTACTGATGTTTGTGTTGATTACGACCTTTATGGTATTACAGGACAAGGTATTTTTAAAGAAGTTTCTGCTGTTTATTATAATAGTTGGCAAAATCTTTTGTATGATTCTAATGGCAACATTATTGGTTTTAAAGATTTTGTTACTAATAAAACATATAATATTTTCCCTTGTTATGCAGGAAGAGTTTCTGCTGCTTTTCATCAAAATGCTTCCTCTTTGGCTTTACTTTATCGTAATTTAAAATGTAGCTATGTTTTGAATAATATTTCTTTAACTACTCAGCCATATTTTGATAGTTATCTTGGTTGCGTTTTTAATGCTGATAATTTAACTGATTATTCTGTTTCTTCTTGTGCTCTTCGCATGGGTAGTGGTTTTTGTGTTGATTATAACTCACCTTCTTCTTCCTCTTCGCGTCGTAAACGTAGAAGTATTTCTGCTTCTTATCGTTTTGTTACTTTTGAACCCTTTAATGTCAGTTTTGTTAATGACAGTATTGAGTCTGTGGGTGGTCTTTATGAGATCAAAATTCCCACTAACTTTACTATAGTTGGTCAAGAGGAATTTATTCAAACTAATTCTCCTAAAGTTACTATTGATTGTTCTTTATTTGTCTGTTCTAATTATGCAGCTTGCCATGACTTATTGTCAGAGTATGGCACTTTTTGTGATAATATTAATAGTATTTTAGATGAAGTTAATGGTTTACTTGATACTACTCAATTGCATGTAGCTGATACTCTTATGCAAGGTGTCACACTTAGCTCCAATCTTAATACTAATTTGCATTTTGATGTTGATAATATTAATTTTAAATCCCTAGTTGGATGTTTAGGTCCACACTGCGGTTCTTCTTCTCGTTCTTTTTTTGAAGATTTATTGTTTGACAAAGTTAAACTTTCAGATGTTGGTTTTGTTGAAGCTTATAACAATTGTACTGGTGGTAGTGAAATTAGAGATCTTCTTTGTGTACAATCCTTTAATGGTATTAAAGTTTTGCCTCCTATTTTGTCTGAATCTCAAATTTCTGGTTACACCACAGCCGCTACTGTTGCTGCTATGTTTCCACCATGGTCAGCAGCAGCTGGCATACCATTTTCTCTTAATGTACAATATAGAATTAATGGTTTGGGTGTTACTATGGATGTTCTTAATAAAAATCAAAAGTTGATAGCTACTGCTTTTAATAATGCTCTTCTTTCTATTCAGAATGGTTTTAGTGCTACCAACTCTGCACTTGCTAAAATACAAAGTGTTGTTAATTCTAATGCTCAAGCACTTAATAGTTTGTTACAGCAATTATTTAATAAATTTGGTGCAATTAGTTCTTCTTTACAAGAAATTTTATCTCGTCTCGATGCTTTAGAGGCTCAGGTTCAGATTGATAGGCTTATTAATGGTCGTTTAACTGCTTTAAATGCTTATGTCTCTCAACAGCTTAGTGATATTTCTCTTGTAAAATTTGGTGCTGCTTTAGCTATGGAGAAGGTTAATGAGTGTGTTAAAAGTCAATCTCCTCGTATTAATTTTTGTGGTAATGGTAATCATATTTTGTCATTAGTTCAAAATGCTCCTTATGGTTTGTTGTTTATGCATTTTAGTTATAAACCTATTTCTTTTAAAACTGTTTTAGTAAGTCCTGGTTTGTGTATATCAGGTGATGTAGGTATTGCACCTAAACAAGGGTATTTTATTAAACATAATGATCATTGGATGTTCACTGGTAGTTCTTACTATTATCCTGAACCAATTTCAGATAAAAATGTTGTTTTTATGAATACTTGTTCTGTTAATTTTACTAAAGCGCCTCTTGTTTATTTGAATCATTCTGTACCAAAATTGTCTGATTTTGAATCTGAGTTATCTCATTGGTTTAAAAATCAAACATCCATTGCGCCTAATTTGACTTTAAATCTTCATACTATTAATGCTACTTTTTTAGATTTGTATTATGAGATGAATCTTATTCAAGAGTCTATTAAGTCTTTGAATAATAGTTATATCAATCTTAAAGATATAGGTACATATGAAATGTATGTAAAATGGCCTTGGTATGTTTGGCTACTAATTTCTTTTTCATTTATAATATTCCTTGTATTGCTCTTTTTTATATGTTGTTGTACTGGTTGTGGTTCTGCATGTTTTAGTAAATGTCATAATTGTTGTGATGAGTATGGTGGTCATCATGATTTTGTTATCAAAACATCTCATGATGATTAG

Protein

MLLIIFILPTTLAVIGDFNCTNFAINDLNTTVPRISEYVVDVSYGLGTYYILDRVYLNTTILFTGYFPKSGANFRDLSLKGTTYLSTLWYQKPFLSDFNNGIFSRVKNTKLYVNKTLYSEFSTIVIGSVFINNSYTIVVQPHNGVLEITACQYTMCEYPHTICKSKGSSRNESWHFDKSEPLCLFKKNFTYNVSTDWLYFHFYQERGTFYAYYADSGMPTTFLFSLYLGTLLSHYYVLPLTCNAISSNTDNETLQYWVTPLSKRQYLLKFDNRGVITNAVDCSSSFFSEIQCKTKSLLPNTGVYDLSGFTVKPVATVHRRIPDLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLVHTDSFSCNNFDESKIYGSCFKSIVLDKFAIPNSRRSDLQLGSSGFLQSSNYKIDTTSSSCQLYYSLPAINVTINNYNPSSWNRRYGFNNFNLSSHSVVYSRYCFSVNNTFCPCAKPSFASSCKSHKPPSASCPIGTNYRSCESTTVLDHTDWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHCAGFGVDEEKCGVLDGSYNVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCSNDLLQPNTEVFTDVCVDYDLYGITGQGIFKEVSAVYYNSWQNLLYDSNGNIIGFKDFVTNKTYNIFPCYAGRVSAAFHQNASSLALLYRNLKCSYVLNNISLTTQPYFDSYLGCVFNADNLTDYSVSSCALRMGSGFCVDYNSPSSSSSRRKRRSISASYRFVTFEPFNVSFVNDSIESVGGLYEIKIPTNFTIVGQEEFIQTNSPKVTIDCSLFVCSNYAACHDLLSEYGTFCDNINSILDEVNGLLDTTQLHVADTLMQGVTLSSNLNTNLHFDVDNINFKSLVGCLGPHCGSSSRSFFEDLLFDKVKLSDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSESQISGYTTAATVAAMFPPWSAAAGIPFSLNVQYRINGLGVTMDVLNKNQKLIATAFNNALLSIQNGFSATNSALAKIQSVVNSNAQALNSLLQQLFNKFGAISSSLQEILSRLDALEAQVQIDRLINGRLTALNAYVSQQLSDISLVKFGAALAMEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLLFMHFSYKPISFKTVLVSPGLCISGDVGIAPKQGYFIKHNDHWMFTGSSYYYPEPISDKNVVFMNTCSVNFTKAPLVYLNHSVPKLSDFESELSHWFKNQTSIAPNLTLNLHTINATFLDLYYEMNLIQESIKSLNNSYINLKDIGTYEMYVKWPWYVWLLISFSFIIFLVLLFFICCCTGCGSACFSKCHNCCDEYGGHHDFVIKTSHDD

Function

attaches the virion to the cell membrane by interacting with host receptor, 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 three 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 which is unmasked following S2 cleavage occurring upon virus endocytosis.
Spike protein S1: attaches the virion to the cell membrane by interacting with host receptor, initiating the infection.
Spike protein S2': Acts as a viral fusion peptide which is unmasked following 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 three 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.

Subunit

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

Miscellaneous

Isolate N1 belongs to genotype A.
Isolate N5 belongs to genotype C. Genotype C probably arose from recombination between genotypes A and B.
Isolate N2 belongs to genotype B.

Similarity

Belongs to the betacoronaviruses spike protein family.

Keywords

3D-structure   Coiled coil   Disulfide bond   Fusion of virus membrane with host endosomal membrane   Fusion of virus membrane with host membrane   Glycoprotein   Host cell membrane   Host membrane   Host-virus interaction   Lipoprotein   Membrane   Palmitate   Signal   Transmembrane   Transmembrane helix   Viral attachment to host cell   Viral envelope protein   Viral penetration into host cytoplasm   Virion   Virulence   Virus entry into host cell  

Feature

chain  Spike glycoprotein

Uniprot

Q5MQD0   Q19U42   Q19U37   S5YGG8   Q0ZJH3   Q19U49   + More
Q19U48   A0A224AU27   U3NAI2   A0A140H1H1   U3N9S7   Q19U47   U3N885   A0A140H1H9   E0YJ44   A0A1Y0EUZ8   S5YA28   A0A451ERM8   Q0ZME7   Q19U40   Q19U39   Q19U45   Q0ZJI1   A0A3G2KXL1   Q14EB0   Q19U46   A0A224ANC9   S5ZBP3   A0A1V0E0Z4   A0A2H4MWY0   A0A3G3NGZ3   A0A2H4MX03   A0A096XNG8   A0A2H4MZ72   A0A2H4MZ10   A0A096XNI4   A0A3G3NHC8   S4WG83   R4WAW7   I2FKH1   A0A0K2RVK5   A0A0K2RVL1   A0A3S7GYI2   B9TXV2   A0A2S0SZ25   A8R4D0   Q83331   S4WIX3   E5RPZ2   S4WLK1   S4WML5   Q6W355   A0A142D826   C6GHR0   C6GHL3   D7PJY2   S4WHI9   A0A5J6NUL2   H9BZX9   A0A5J6NRR8   S4WG91   S4WG99   B7TYG9   H9AA34   B7U2L1   B3VTS5   Q0PL39   S4WIX5   A0A346I7G9   H9AA55   S4WG79   Q2EEY3   S4WLK8   A0A481S1P4   S4WLK4   P25192   B7U2R5   B7U2N3   F1T0N1   B7U2M2   B7U2S7   S4WG94   A0A142D823   A0A142D820   E3UTE9   A4ZU41   S4WLL0   A6YD40   Q58NS2   A0A142D831   Q9QD01   C6GHP9   S4WHJ6   A0A346I7H0   A0A481S1B7   A0A2R4STR1   A0A142D818   B9TXU9   Q58NS1   A0A142D828  

Pubmed

15613317    16757599    16809319    24394697    29217279    20719951    + More
30285857    25463600    23804565    23648375    26271151    17706262    7785316    21273011    26969241    20519394    31534035    22398294    18842722    16954245    30771080    2053289    21430123    20880639    17669602    15681072   

EMBL

AY597011    DQ415896    DQ415904    DQ415905    DQ415906    DQ415907    + More
DQ415914    DQ437613    DQ437614    ABD75497.1    ABD75561.1    ABD75569.1    ABD75577.1    ABD75585.1    ABD75641.1    ABD96192.1    ABD96193.1    DQ415900    DQ415901    DQ437618    DQ437619    KF430198    ABD75529.1    ABD75537.1    ABD96197.1    ABD96198.1    AGT17763.1    KF430203    AGT17777.1    DQ415903    ABD75553.1    DQ415908    DQ437607    ABD75593.1    ABD96186.1    DQ415909    DQ437608    ABD75601.1    ABD96187.1    LC315650    BBA20983.1    KF686340    KF686341    KF686342    KF686346    KY674941    KY674942    KY674943    AGW27836.1    AGW27845.1    AGW27854.1    AGW27881.1    ARB07599.1    ARB07608.1    ARB07617.1    KT779555    AMN88686.1    KF686344    AGW27872.1    DQ415910    DQ437609    ABD75609.1    ABD96188.1    KF686343    AGW27863.1    KT779556    AMN88694.1    HM034837    ADN03339.1    KY983584    ARU07577.1    KF430201    AGT17769.1    MK167038    AZS52618.1    DQ339101    DQ415898    DQ437616    ABD75513.1    ABD96195.1    DQ415897    DQ415899    DQ415913    DQ437612    DQ437615    DQ437617    ABD75505.1    ABD75521.1    ABD75633.1    ABD96191.1    ABD96194.1    ABD96196.1    DQ415912    DQ437611    ABD75625.1    ABD96190.1    DQ415902    ABD75545.1    MH940245    AYN64561.1    AY884001    DQ415911    DQ437610    ABD75617.1    ABD96189.1    LC315651    BBA20986.1    KF430197    AGT17758.1    KY674921    ARB07438.1    KY370043    ATP66727.1    MH687968    AYR18599.1    KY370048    ATP66756.1    KF294370    AID16649.1    KY370051    ATP66773.1    KY370049    ATP66762.1    KF294371    AID16655.1    MH687970    AYR18616.1    KF169920    AGO98871.1    AB775894    BAN18703.1    AB671299    BAM15656.1    LC061273    BAS18856.1    LC061274    BAS18866.1    MG757144    AVI15053.1    EU401989    ACB30203.1    MF416379    AWB14621.1    EF446615    ABP87990.1    U14646    AAA87063.1    KF169932    AGO98883.1    AB555560    LC061272    BAJ52885.1    BAS18846.1    KF169923    AGO98874.1    KF169931    AGO98882.1    AY316300    AAQ67205.1    KT318119    KT318120    AMQ23495.1    AMQ23496.1    FJ938067    ACT11030.1    FJ938063    ACT10983.1    GU593319    ADI59790.1    KF169924    AGO98875.1    MN514970    QEY10672.1    JQ173883    AFD97607.1    MN514971    QEY10673.1    KF169930    AGO98881.1    KF169939    KF169940    AGO98890.1    AGO98891.1    FJ415324    ACJ35486.1    JN874559    AFE48795.1    FJ425184    ACJ66946.1    EU814647    ACF21935.1    DQ811784    ABG89288.1    KF169937    AGO98888.1    MH197037    MH197038    MH203065    AXP11688.1    AXP11689.1    AXP11697.1    JN874561    AFE48817.1    KF169915    AGO98866.1    DQ389658    ABD18934.1    KF169933    AGO98884.1    MK046003    QBG67072.1    KF169927    KF169928    KF169929    AGO98878.1    AGO98879.1    AGO98880.1    AF058942    FJ425189    ACJ67000.1    FJ425186    ACJ66971.1    AB593383    BAK18575.1    FJ425185    ACJ66961.1    FJ425190    ACJ67012.1    KF169935    AGO98886.1    KT318116    AMQ23492.1    KT318113    AMQ23489.1    HM573327    HM573328    HM573329    HM573330    ADP21336.1    ADP21337.1    ADP21338.1    ADP21339.1    EF424621    ABP38306.1    KF169938    AGO98889.1    EF445634    ABP73656.1    AY935637    AAX38489.1    KT318124    AMQ23500.1    AF190406    AAF05704.1    FJ938066    ACT11019.1    KF169934    AGO98885.1    MH197039    AXP11690.1    MK046010    QBG67079.1    MH043952    AVZ61099.1    KT318111    AMQ23487.1    EU401986    ACB30200.1    AY935638    AAX38490.1    KT318121    AMQ23497.1   

Proteomes

UP000008170    UP000102058    UP000103177    UP000107950    UP000118444    UP000123677    + More
UP000161305    UP000120443    UP000147573    UP000148743    UP000164754    UP000174991    UP000098607    UP000143896    UP000173725    UP000173897    UP000122230    UP000127413    UP000168247    UP000139452    UP000134208    UP000108760    UP000098016    UP000001985    UP000107997    UP000143869    UP000156925    UP000168964    UP000134743    UP000124867    UP000006551    UP000162514    UP000130220    UP000155347    UP000103372    UP000166748    UP000164707    UP000172225    UP000117254    UP000118088    UP000158296    UP000107676    UP000174569    UP000147981    UP000125269    UP000133443    UP000140344    UP000104294    UP000102696    UP000136116    UP000162935   

PRIDE

Q5MQD0    Q0ZME7    Q14EB0    P25192   

Pfam

PF09408   Spike_rec_bind
PF01601   Corona_S2
PF16451   Spike_NTD

Interpro

IPR027400   S_HR2
IPR043002   Spike_N_sf
IPR042578   BETA_CORONA_SPIKE
IPR036326   Spike_rcpt-bd_sf
IPR002552   Corona_S2
IPR018548   Spike_rcpt-bd
IPR032500   Spike_N

SUPFAM

SSF143587   SSF143587

Gene 3D

1.20.5.790     2.60.120.960    

ProteinModelPortal

Q5MQD0   Q19U42   Q19U37   S5YGG8   Q0ZJH3   Q19U49   + More
Q19U48   A0A224AU27   U3NAI2   A0A140H1H1   U3N9S7   Q19U47   U3N885   A0A140H1H9   E0YJ44   A0A1Y0EUZ8   S5YA28   A0A451ERM8   Q0ZME7   Q19U40   Q19U39   Q19U45   Q0ZJI1   A0A3G2KXL1   Q14EB0   Q19U46   A0A224ANC9   S5ZBP3   A0A1V0E0Z4   A0A2H4MWY0   A0A3G3NGZ3   A0A2H4MX03   A0A096XNG8   A0A2H4MZ72   A0A2H4MZ10   A0A096XNI4   A0A3G3NHC8   S4WG83   R4WAW7   I2FKH1   A0A0K2RVK5   A0A0K2RVL1   A0A3S7GYI2   B9TXV2   A0A2S0SZ25   A8R4D0   Q83331   S4WIX3   E5RPZ2   S4WLK1   S4WML5   Q6W355   A0A142D826   C6GHR0   C6GHL3   D7PJY2   S4WHI9   A0A5J6NUL2   H9BZX9   A0A5J6NRR8   S4WG91   S4WG99   B7TYG9   H9AA34   B7U2L1   B3VTS5   Q0PL39   S4WIX5   A0A346I7G9   H9AA55   S4WG79   Q2EEY3   S4WLK8   A0A481S1P4   S4WLK4   P25192   B7U2R5   B7U2N3   F1T0N1   B7U2M2   B7U2S7   S4WG94   A0A142D823   A0A142D820   E3UTE9   A4ZU41   S4WLL0   A6YD40   Q58NS2   A0A142D831   Q9QD01   C6GHP9   S4WHJ6   A0A346I7H0   A0A481S1B7   A0A2R4STR1   A0A142D818   B9TXU9   Q58NS1   A0A142D828  

PDB

5I08     E-value=0,     Score=5278