Strain

USA_MURINE_2009_NC_012936 (Region: USA;  Strain: Rat coronavirus Parker, complete genome.;  Date: 2009)

Gene

spike protein

Description

Annotated in NCBI,  spike protein

Location

NC_012936(+):23891-27973

GenBank Accession

YP_003029848.1

Full name

Spike glycoprotein      

Alternative Name

E2
Peplomer protein

CDS

ATGCTATTCGTGTTTTTAACCCTATTGCCCTCTTGTCTAGGGTATATTGGTGATTTTAGATGTATCAACCGTGTAAACACCAGCATTTCTAATGCGCGCGCACCCAGTGTTAGCACAGAGGTAGTTGATGTTTCTAAAGGTCTTGGTACATATTACGTTTTAGATCGCGTTTATTTAAATGCCACATTATTGCTTACTGGTTACTACCCTGTACATGGGTCCATGTATCGTAACATGGCTCTAATGGGTACTAATACCTTAAGCCTTAATTGGTTTGAACCGCCCTTTTTATCAGAGTTTAACGATGGCATATATGCTAAGGTAAAGAACCTTAAAGCATCTTTGCCCATAGGCTCGGCTTCATACTTTCCTACTATAATTATAGGTAGTAATTTTGTTAATACTTCCTATACTGTAGTATTGGAACCATACAATGGTATTATTATGGCATCTATTTGCCAGTATACCATTTGTCAATTACCGCACACGTATTGCAAACCTAATACGGGCGGTAACACGCTAATTGGTTTTTGGCACACAGATTTAAGGTCTCCGGTGTGCATTTTAACGCGTAATTTTACGTTTAATGTTAATGCCGAATGGCTTTATTTTCATTTTTATCAGCAGGGTGGTACTTTTTATGCGTATTATGCAGATGTTTCTTCTGCCACTACGTTTTTGTTTAGTTCGTATATTGGTGCTGTGTTAACACAGTATTTTGTGTTGCCTTATATGTGTAATCCCACTACCTCAGGTGTTTTCTCACCGCAGTATTGGGTTACACCTCTTGTTAAGCGCCAATATTTATTTAATTTTAACCAAAAGGGTATTATTACTAGCGCAGTTGATTGTGCTAGTAGTTATACCAGTGAAATAAAGTGTAAGACTCAAAGTATGAATCCCAATACGGGAGTCTATGATTTATCCGGTTACACCGTCCAACCTGTAGGACTAGTGTACCGGCGTGTTAGAAATTTGCCTGATTGTAAAATTGAGGAATGGCTTGCTGCTAACACAGTACCCTCTCCTCTCAATTGGGAGCGCAAAACATTTCAAAATTGTAACTTCAACCTGAGCAGTCTATTAAGATTTGTTCAGGCTGAGTCACTCTCATGTAGTAATATAGATGCTTCCAAGGTTTATGGAATGTGCTTTGGTAGCATATCTATAGATAAATTTGCAATACCCAACAGTCGCCGTGTTGATCTTCAGCTAGGTAAATCGGGTCTTTTGCAATCTTTTAACTATAAAATTAGTACAAGAGCGACCTCGTGTCAGCTCTATTACAGTCTTGCACAAAATAATGTCACTGTCATTAACCACAACCCATCCTCCTGGAATAGGCGTTATGGATTTAATGACGTGGCTACATTTGGTAGTGGTATACATGACGTGGCTTATGCAGAGGCATGTTTCACTGTTGGAGCTTCATATTGCCCTTGTGCGAAGCCCAGCATAGTCTATTCATGTGTCACAGGTAAACCTAAGTCTGCTAATTGCCCAACAGGTACCTCGCATCGTGAGTGTAATGTTCAGGCTTCAGGTTTTAAGCATAAGTGCGATTGCACATGTAACCCTAGTCCTCTAACCACCTATGATCCTAGATGTCTTCAAGCGCGGAGCATGCTTGGCGTAGGTGATCATTGTGAGGGTCTAGGTATTTTAGAAGATAAATGTGGTGGCAGCAACATATGCAATTGTTCGGCTGATGCCTTTGTTGGCTGGGCTAAGGACAGTTGTCTATCTAATGACCGCTGCCATATTTTTAGTAATTTGATGTTAAATGGCATTAATAGTGGTACTACATGTTCCACTGATCTGCAATTGCCTAATACGGAAGTGGTCACTGGCGTTTGTGTCAAGTATGACCTCTACGGTATTACAGGCCAAGGTGTTTTTAAGGAGGTTAAGGCTGATTATTATAATAGTTGGCAGAACCTCTTATATGATGTTAATGGTAACTTAAATGGTTTCCGTGACATTGTTACTAATAAGACTTATTTATTAAGAAGTTGCTATAGTGGGCGCGTTTCGGCTGCATATCATCAAGATGCACCTGAACCAGCGCTACTATATCGCAATTTAAAATGTGATTATGTGTTTAATAACAACATATCCCGTGAGGAGACACCACTTAACTATTTTGATAATTATTTGGGTTGTGTTGTTAATGCTGATAACTCAACTGAGCATTCTGTTGACGCGTGTGATTTGCGTATGGGTAGTGGGCTCTGTGTCAACTATTCAACCGCTCACCGTGCTCGTAGGTCTGTCAGTACGGGTTATAAATTAACTACTTTTGAACCATTTACAGTCAGCATTGTCAATGATAGTGTTGAGTCTGTAGGTGGATTATATGAGATGCAAATACCTACCAATTTTACTATAGCTAGCCAGCAGGAGTTTATTCAAACGAGGTCTCCGAAGGTTACTATAGATTGTGCTGCATTTGTCTGTGGCGATTATACAGTGTGTAGACAACAGTTGGTTGATTATGGCTCTTTTTGTGATAATATTAATGCCATTCTTGGCGAGGTGAATAACCTCATAGATACTATGCAACTACAAGTTGCTAGTGCTCTGATCCAAGGTGTCACGCTAAATTCACGCTTGGCAGATGGCATCTCAGGTCAGATTGATGATATTAATTTTAGCCCTCTTCTAGGTTGCCTTGGCTCATATTGCAGCGAAGGCACCATGGCAGTGCAAGGGCGATCTGCTATAGAGGATGTATTATTTGATAAGGTCAAACTCTCTGATGTTGGCTTTGTCGAAGCATATAATAATTGCACTGGAGGTCAAGAAGTTAGAGACCTACTTTGTGTGCAATCTTTCAATGGCATTAAAGTGCTACCGCCTGTATTATCCGAGAGTCAAATCTCTGGTTATACAGCGGGAGCTACTGCATCTGCTATGTTCCCTCCATGGTCTGCAGCTGCAGGTGTGCCATTTGCTTTAAGTGTTCAATATAGAATTAATGGTCTTGGTGTCACTATGAATGTTCTTAGTGAAAACCAGAAAATGATAGCTAGTTCATTTAACAACGCGATAGGTGCTATACAGGAAGGGTTCGATGCTACCAATTCTGCTTTAGCGAAAATTCAGTCCGTTGTCAATTCAAATGCAGAAGCACTCAATAACCTTTTGAATCAGCTTTCCAATAGGTTTGGTGCAATTAGTGCTTCTTTACAGGAAATTCTATCCCGCCTTGATGCTCTTGAAGCGCAGGCTCAGATAGACCGTCTTATTAATGGCAGATTAACTGCACTTAATGCATATGTATCTAAGCATCTGAGCGACATGACCCTTATTAAGGTGAGTGCTGCCCAGGCTATAGAGAAAGTTAATGAGTGTGTTAAAAGCCAATCACCTAGGATAAATTTCTGTGGCAATGGCAATCATATATTGTCATTAGTCCAGAATGCGCCTTACGGTTTATATTTTATTCATTTCAGCTATGTGCCCACATCCTTTACAACGGTAAATGTGAGTCCTGGACTATGCATTTCTGGTGATAGAGGATTAGCACCTAAAGCTGGATATTTTGTTCAAGATCATGGAGAATGGAAGTTCACAGGTAGCAATTATTACTACCCTGAATCCATTACAGATAAAAACAGTGTCGTGATGAGTAGTTGCGCAGTAAACTACACAAAGGCACCTGAAGTTTTCTTGAACACTTCAATAACTAATCTACCCGACTTTAAGGAGGAGTTAGATAAATGGTTTAAGAATCAGACGTCTATTGTGCCTGATTTATCTTTCGATATCGGGAAATTAAATGTTACATTCCTTGACCTGTCCTATGAGATGAACAGGATTCAGGATGCAATTAAGAATTTAAATGAGAGTTACATCAACCTCAAGGAAATTGGCACATATGAGATGTATGTGAAATGGCCTTGGTATGTTTGGCTGCTAATTGGATTAGCTGGTGTAGCTGTTTGTGTTTTGTTATTTTTTATATGTTGCTGCACAGGTTGTGGCTCTTGTTGTTTTAAGAAATGTGGAAATTGTTGTGATGAGTATGGAGGACGTCAGGCAGGTATTGTGATACATAATATTTCCTCTCATGAGGATTGA

Protein

MLFVFLTLLPSCLGYIGDFRCINRVNTSISNARAPSVSTEVVDVSKGLGTYYVLDRVYLNATLLLTGYYPVHGSMYRNMALMGTNTLSLNWFEPPFLSEFNDGIYAKVKNLKASLPIGSASYFPTIIIGSNFVNTSYTVVLEPYNGIIMASICQYTICQLPHTYCKPNTGGNTLIGFWHTDLRSPVCILTRNFTFNVNAEWLYFHFYQQGGTFYAYYADVSSATTFLFSSYIGAVLTQYFVLPYMCNPTTSGVFSPQYWVTPLVKRQYLFNFNQKGIITSAVDCASSYTSEIKCKTQSMNPNTGVYDLSGYTVQPVGLVYRRVRNLPDCKIEEWLAANTVPSPLNWERKTFQNCNFNLSSLLRFVQAESLSCSNIDASKVYGMCFGSISIDKFAIPNSRRVDLQLGKSGLLQSFNYKISTRATSCQLYYSLAQNNVTVINHNPSSWNRRYGFNDVATFGSGIHDVAYAEACFTVGASYCPCAKPSIVYSCVTGKPKSANCPTGTSHRECNVQASGFKHKCDCTCNPSPLTTYDPRCLQARSMLGVGDHCEGLGILEDKCGGSNICNCSADAFVGWAKDSCLSNDRCHIFSNLMLNGINSGTTCSTDLQLPNTEVVTGVCVKYDLYGITGQGVFKEVKADYYNSWQNLLYDVNGNLNGFRDIVTNKTYLLRSCYSGRVSAAYHQDAPEPALLYRNLKCDYVFNNNISREETPLNYFDNYLGCVVNADNSTEHSVDACDLRMGSGLCVNYSTAHRARRSVSTGYKLTTFEPFTVSIVNDSVESVGGLYEMQIPTNFTIASQQEFIQTRSPKVTIDCAAFVCGDYTVCRQQLVDYGSFCDNINAILGEVNNLIDTMQLQVASALIQGVTLNSRLADGISGQIDDINFSPLLGCLGSYCSEGTMAVQGRSAIEDVLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTAGATASAMFPPWSAAAGVPFALSVQYRINGLGVTMNVLSENQKMIASSFNNAIGAIQEGFDATNSALAKIQSVVNSNAEALNNLLNQLSNRFGAISASLQEILSRLDALEAQAQIDRLINGRLTALNAYVSKHLSDMTLIKVSAAQAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLYFIHFSYVPTSFTTVNVSPGLCISGDRGLAPKAGYFVQDHGEWKFTGSNYYYPESITDKNSVVMSSCAVNYTKAPEVFLNTSITNLPDFKEELDKWFKNQTSIVPDLSFDIGKLNVTFLDLSYEMNRIQDAIKNLNESYINLKEIGTYEMYVKWPWYVWLLIGLAGVAVCVLLFFICCCTGCGSCCFKKCGNCCDEYGGRQAGIVIHNISSHED

Function

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.
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.

Subunit

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

Miscellaneous

The viral fusion process requires lipid rafts of the host plasma membrane (By similarity). This strain is apparently capable of entering cells either through direct fusion at the cell surface or through endocytosis.

Similarity

Belongs to the betacoronaviruses spike protein family.

Keywords

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   3D-structure  

Feature

chain  Spike protein S2

Uniprot

C6GHS2   I1TMH2   I1TMG2   Q9IKD1   Q83331   D7PJY2   + More
H9BZX9   A0A2S0SZ25   F1T0N1   O55253   Q9QD01   Q5ICX2   Q77NN1   P90210   Q77NQ7   A7U544   C0KYW1   A0A096XNH1   D4QFK1   Q83330   C0KYX0   C0KYS1   C0KYU0   P22432   C0KYT1   C0KYY9   Q02385   Q6RI11   Q6RI10   A0A2H4MWY0   A0A096XNG8   A0A096XNI4   A0A2H4MZ72   A0A2H4MX03   A0A3G3NGZ3   A0A2H4MZ10   A0A3G3NHC8   A8R4D0   I2FKH1   R4WAW7   A0A0K2RVK5   Q6W355   A0A0K2RVL1   E5RPZ2   A0A2H4MXF2   C6GHR0   B7TYG9   A0A3Q9JZN4   A0A2R4STS2   A4ZU41   H9AA34   A4ZTX5   A0A2R4STR1   A4ZU74   A4ZU63   H9AA55   A4ZU52   A0A481S1P4   A0A346I7G9   Q8V436   B7U2R5   B7U2N3   B7U2M2   B7U2S7   S4WHI0   B7U2L1   S4WML5   A0A3S9Y2D8   E3UTE9   H9AA44   A0A2R4STT0   Q91A26   E3UTE8   Q2EF08   B9TXU9   A0A451EU06   S4WLK4   A0A346I7H0   A6YD40   P25192   A0A5J6NUG7   A0A2H4MXV6   S4WIX3   B7U2P4   A0A346I7H6   A0A142D820   C6GHM5   A0A5J6NUL2   C6GHN7   A4ZU30   S4WLK1   A0A142D831   A0A481S1B7   S4WG79   Q2EF04   B7U2Q4   S4WG91   A0A142D828   S4WG99   Q9QAQ8  

Pubmed

10882653    7785316    20519394    21430123    15507445    11582515    + More
9007076    11502093    20631137    17041219    25463600    17079303    2556846    1966429    9201212    10438865    12970410    1316938    15308703    30285857    17706262    23648375    26271151    21273011    22398294    17434558    17344285    30771080    11714968    18842722    23804565    20880639    17803510    17669602    2053289    31534035    26969241    9778786   

EMBL

FJ938068    ACT11042.1    JF792617    AFG25760.1    JF792616    AFG25750.1    + More
AF207551    U14646    AAA87063.1    GU593319    ADI59790.1    JQ173883    AFD97607.1    MF416379    AWB14621.1    AB593383    BAK18575.1    AB008940    BAA23719.1    AF190406    AAF05704.1    AY771998    AAW47240.1    AF207902    AAF68923.1    U72635    AAC56567.1    AF201929    AAF19386.1    EF682498    ABS87264.1    FJ647223    ACN89742.1    KF294372    AID16661.1    AB551247    BAJ04696.1    U14645    AAA87062.1    FJ647224    ACN89743.1    FJ647219    ACN89696.1    FJ647221    ACN89722.1    M32789    S51114    FJ647220    ACN89705.1    FJ647226    ACN89763.1    D10235    AY497330    AAR92027.1    AY497331    AAR92028.1    KY370043    ATP66727.1    KF294370    AID16649.1    KF294371    AID16655.1    KY370051    ATP66773.1    KY370048    ATP66756.1    MH687968    AYR18599.1    KY370049    ATP66762.1    MH687970    AYR18616.1    EF446615    ABP87990.1    AB671299    BAM15656.1    AB775894    BAN18703.1    LC061273    BAS18856.1    AY316300    AAQ67205.1    LC061274    BAS18866.1    AB555560    LC061272    BAJ52885.1    BAS18846.1    KY370052    ATP66779.1    FJ938067    ACT11030.1    FJ415324    ACJ35486.1    MK095174    AZS64221.1    MH043953    AVZ61109.1    EF424621    ABP38306.1    JN874559    AFE48795.1    EF424615    ABP38236.1    MH043952    AVZ61099.1    EF424624    ABP38334.1    EF424623    ABP38328.1    JN874561    AFE48817.1    EF424622    ABP38313.1    MK046003    QBG67072.1    MH197037    MH197038    MH203065    AXP11688.1    AXP11689.1    AXP11697.1    AF391542    FJ425189    ACJ67000.1    FJ425186    ACJ66971.1    FJ425185    ACJ66961.1    FJ425190    ACJ67012.1    KF169914    AGO98865.1    FJ425184    ACJ66946.1    KF169931    AGO98882.1    MK095175    AZS64222.1    HM573327    HM573328    HM573329    HM573330    ADP21336.1    ADP21337.1    ADP21338.1    ADP21339.1    JN874560    AFE48805.1    MH043954    MK095180    AVZ61119.1    AZS64227.1    AF391541    HM573326    ADP21335.1    DQ389633    ABD18909.1    EU401986    ACB30200.1    MK095186    AZS64233.1    KF169927    KF169928    KF169929    AGO98878.1    AGO98879.1    AGO98880.1    MH197039    AXP11690.1    EF445634    ABP73656.1    AF058942    MN514962    QEY10625.1    KY370046    ATP66744.1    KF169932    AGO98883.1    FJ425187    ACJ66977.1    MH203064    AXP11696.1    KT318113    AMQ23489.1    FJ938064    ACT10995.1    MN514970    QEY10672.1    FJ938065    ACT11007.1    EF424620    ABP38295.1    KF169923    AGO98874.1    KT318124    AMQ23500.1    MK046010    QBG67079.1    KF169915    AGO98866.1    DQ389637    ABD18913.1    FJ425188    ACJ66990.1    KF169930    AGO98881.1    KT318121    AMQ23497.1    KF169939    KF169940    AGO98890.1    AGO98891.1    AF058944   

Proteomes

UP000173347    UP000161770    UP000175084    UP000117254    UP000118088    UP000163097    + More
UP000139707    UP000159025    UP000154289    UP000167944    UP000158592    UP000133456    UP000098534    UP000148943    UP000103372    UP000130220    UP000155347    UP000166748    UP000164707    UP000158296    UP000136116    UP000107676    UP000121953    UP000147178    UP000163913    UP000125269    UP000139235    UP000008571    UP000133443    UP000140344    UP000104294    UP000102696    UP000174569    UP000124585    UP000008570    UP000158327    UP000136745    UP000139966    UP000170940    UP000148210   

PRIDE

P22432    Q02385    Q8V436    Q91A26    P25192    Q9QAQ8    + More

Pfam

PF09408   Spike_rec_bind
PF01601   Corona_S2
PF16451   Spike_NTD

Interpro

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

SUPFAM

SSF143587   SSF143587

Gene 3D

1.20.5.790     2.60.120.960    

ProteinModelPortal

C6GHS2   I1TMH2   I1TMG2   Q9IKD1   Q83331   D7PJY2   + More
H9BZX9   A0A2S0SZ25   F1T0N1   O55253   Q9QD01   Q5ICX2   Q77NN1   P90210   Q77NQ7   A7U544   C0KYW1   A0A096XNH1   D4QFK1   Q83330   C0KYX0   C0KYS1   C0KYU0   P22432   C0KYT1   C0KYY9   Q02385   Q6RI11   Q6RI10   A0A2H4MWY0   A0A096XNG8   A0A096XNI4   A0A2H4MZ72   A0A2H4MX03   A0A3G3NGZ3   A0A2H4MZ10   A0A3G3NHC8   A8R4D0   I2FKH1   R4WAW7   A0A0K2RVK5   Q6W355   A0A0K2RVL1   E5RPZ2   A0A2H4MXF2   C6GHR0   B7TYG9   A0A3Q9JZN4   A0A2R4STS2   A4ZU41   H9AA34   A4ZTX5   A0A2R4STR1   A4ZU74   A4ZU63   H9AA55   A4ZU52   A0A481S1P4   A0A346I7G9   Q8V436   B7U2R5   B7U2N3   B7U2M2   B7U2S7   S4WHI0   B7U2L1   S4WML5   A0A3S9Y2D8   E3UTE9   H9AA44   A0A2R4STT0   Q91A26   E3UTE8   Q2EF08   B9TXU9   A0A451EU06   S4WLK4   A0A346I7H0   A6YD40   P25192   A0A5J6NUG7   A0A2H4MXV6   S4WIX3   B7U2P4   A0A346I7H6   A0A142D820   C6GHM5   A0A5J6NUL2   C6GHN7   A4ZU30   S4WLK1   A0A142D831   A0A481S1B7   S4WG79   Q2EF04   B7U2Q4   S4WG91   A0A142D828   S4WG99   Q9QAQ8  

PDB

3JCL     E-value=0,     Score=5178