Strain
Human_OC43_MN026164
(Region: Kenya; Strain: Human coronavirus OC43 isolate OC43_KLF_01_2018, complete genome.; Date: 18-Jan-18)
Gene
S
Description
Annotated in NCBI,
S
Location
GenBank Accession
Full name
Spike glycoprotein
Alternative Name
E2
Peplomer protein
Peplomer protein
Sequence
CDS
ATGTTTTTGATACTTTTAATTTCCTTACCAACGGCTTTTGCTGTTATAGGAGATTTAAATTGTACTTTAGATCCTAGGCTTAAAGGTAGCTTTAATAATAGAGACACCGGTCATCCTTCTATAAGTACTGATACTGTTGATGTTACTAATGGTTTGGGTACTTATTATGTTTTAGATCGTGTGTATTTAAATACCACATTGTTTCTTAATGGTTATTACCCCACTTCAGGTTCCACATATCGTAATATGGCACTGAAGGGAACTGACTTATTGAGCACATTATGGTTTAAACCACCATTTCTTTCTGATTTTATTAATGGTATTTTTGCTAAGGTCAAAAATACCAAGGTTTTTATAGATGGTGTAATGTATAGTGAGTTCCCTGCTATAACTATAGGTAGTACTTTTGTAAATACATCCTATAGTGTGGTAGTACAACCACGTACAATTAATTCAACACAGGATGGTGTTAATAAATTACAAGGTCTTTTAGAGGTCTCTGTTTGCCAGTATAATATGTGTGAGTACCCACATACGATTTGTCATCCTAACTTGGGTAACCATTTCAAAGAACTATGGCATTATGATACAGGCGTTGTTTCCTGTTTGTATAAGCGTAATTTCACATATGATGTGAATGCTACTTATTTGTATTTTCATTTTTATCAAGAAGGTGGTACTTTTTATGCATATTTTACAGACACTGGTTTTGTTACTAAGTTTTTGTTTAATGTTTATTTAGGCATGGCACTTTCACACTATTATGTCATGCCTCTGACTTGTATTCGTAGGGCTAAACACGGTTTTAGTTTAGAATATTGGGTTACACCCCTCACTCCTAGACAATATTTACTCGCTTTCAATCAAGATGGTATTATTTTTAATGCTGTTGATTGTATGAGTGATTTTATGAGTGAGATTAAGTGTAAAACACAATCTATAGCACCACCCACTGGTGTTTATGAATTAAACGGTTACACTGTTCAGCCAATTGCAGATGTTTACCGACGCAAACCTGATCTTCCCAATTGTAATATAGAAGCTTGGCTTAATGATAAGTCGGTGCCCTCCCCATTAAATTGGGAACGTAAGACATTTTCAAATTGTAATTTTAATATGAGCAGCCTGATGTCTTTTATTCAGGCAGACTCATTTACTTGTAATAATATTGATGCTGCTAAGATATATGGTATGTGTTTTTCCAGCATAACTATAGATAAGTTTGCTATACCCAATCGCAGGAAGGTTGACCTACAATTGGGTAATTTGGGCTATTTGCAGTCATCCAACTATAGAATTGATACTACTGCAACAAGTTGTCAGTTGTATTATAATTTACCTGCTGCTAATGTCTCTGTTAGCAGGTTTAATCCTTCTACTTGGAATAAGAGATTTGGTTTTATAGAAGATTCTGTTTTTGTGCCTCAACCTACAGGTGTTTTTACTAATCACAGTGTAGTTTATGCACAACACTGTTTTAAAGCCCCTAAAAATTTCTGTCCGTGTAGTTCCTGTCCTAGTAAAAATAATGGTATAGGCACTTGTCCTGCAGGTACTAATTCTTTAACTTGTGATAATTTATGTACTCTTGATCCTATTACACTTAAAGCTCCAGATACTTATAAGTGCCCCCAATCTAAATCTTTAGTTGGTATAGGTGAGCACTGTTCGGGTCTTGCTGTTAAAAGTGATTATTGTGGAAACAATTCTTGTACTTGCCAACCACAAGCATTTTTGGGTTGGTCTGCAGACTCTTGTTTACAAGGAGACAAGTGTAATATTTTTGCTAATTTCATTTTGCATGATGTTAATAATGGTCTTACTTGTTCTACTGATTTACAAAAAGCTAACACAGAAATAGAACTTGGTGTTTGTGTTAATTATGACCTCTATGGTATTTCTGGCCAAGGCATTTTTGTTGAGGTTAATGCGACTTATTATAATAGTTGGCAGAACCTTTTATATGATTCTAATGGTAACCTCTACGGTTTTAGAGACTACATAACAAACAGAACTTTTATGATTCATAGTTGCTATAGCGGTCGTGTTTCTGCGGCCTATCATGCCAACTCTTCCGAACCAGCATTGCTATTTCGGAATATTAAATGCAACTACGTTTTTAATAATAGTCTTACACGACAGCTGCAACCCATTAACTATTCGTTTGATAGTTATCTTGGTTGTGTTGTCAATGCTTATAATAGTACTGCTATTTCTGTCCAAACATGTGATCTCACAGTAGGTAGTGGTTACTGTGTGGATTACTCTAAAAATAGACGAAGTCGTAGAGCGATCACCACTGGTTATCGGTTTACTAATTTTGAGCCATTTACTGTTAATTCAGTAAATGATAGTTTGGAACCTGTAGGTGGTTTGTATGAAATTCAAATACCTTCAGAGTTTACTATAGGTAATATGGAGGAGTTTATTCAAACAAGCTCTCCCAAAGTTACTATTGATTGTGCTGCATTTGTCTGTGGTGATTATGCAGCATGTAAATTACAGTTGGTTGAATATGGTAGTTTCTGTGATAACATTAATGCCATACTCACAGAAGTAAATGAACTACTTGATACTACACAGTTGCAAGTAGCTAATAGTTTAATGAATGGTGTTACTCTTAGCACTAAGCTTAAAGATGGTGTTAATTTCAATGTAGACGACATCAATTTTTCCCCTGTATTAGGTTGTCTAGGCAGCGAATGTAGTAAAGCTTCCAGTAGATCTGCTATAGAGGATTTACTTTTTGATAAAGTAAAGTTATCTGATGTCGGTTTCGTTGAGGCTTATAATAATTGTACAGGAGGTGCCGAAATTAGGGACCTCATTTGTGTGCAAAGTTATAAAGGCATCAAAGTGTTGCCTCCACTGCTCTCAGAAAATCAGATCAGTGGATATACTTTGGCTGCCACCTCTGCTAGTCTATTTCCTCCTTGGACAGCAGCAGCAGGTGTACCATTTTATTTAAATGTTCAGTATCGCATTAATGGGCTTGGTGTCACCATGGATGTGCTAAGTCAAAATCAAAAGCTTATTGCTAATGCATTTAACAATGCCCTTCATGCTATTCAGCAAGGGTTCGATGCAACTAATTCTGCTTTAGTTAAAATTCAAGCTGTTGTTAATGCAAATGCTGAAGCTCTTAATAACTTATTGCAACAACTCTCTAATAGATTTGGTGCTATAAGTGCTTCTTTACAAGAAATTCTATCTAGACTTGATGCTCTTGAAGCGGAAGCTCAGATAGATAGACTTATTAATGGTCGTCTCACCGCTCTTAATGCTTATGTTTCTCAACAGCTTAGTGATTCTACACTGGTAAAATTTAGTGCAGCACAAGCTATGGAGAAGGTTAATGAATGTGTCAAAAGCCAATCATCTAGGATAAATTTCTGTGGTAATGGTAATCATATTATATCATTAGTGCAGAATGCTCCATATGGTTTGTATTTTATCCACTTTAATTATGTCCCTACTAAGTATGTCACAGCGAAGGTTAGTCCTGGTCTGTGCATTGCTGGTAATAGAGGTATAGCTCCTAAGAGTGGTTATTTTGTTAATGTAAATAATACTTGGATGTACACTGGTAGTGGTTACTACTACCCTGAACCTATAACTGAAAATAATGTTGTTGTTATGAGTACCTGCGCTGTTAATTATACTAAAGCGCCGTATGTAATGCTGAACACCTCAATACCCAACCTTCCTGATTTTAAGGGAGAGTTGGACCAATGGTTCAAAAATCAAACATCAGTGGCACCAGATTTGTCACTTGATTATATAAATGTTACATTCTTGGACCTACAAGTTGAAATGAATAGGTTACAGGAGGCAATAAAAGTTTTAAATCATAGCTACATCAATCTCAAGGACATTGGTACATATGAATATTATGTAAAATGGCCTTGGTATGTATGGCTTTTAATCTGCCTTGCTGGTGTAGCTATGCTTGTTTTACTATTCTTCATATGCTGTTGTACAGGATGTGGGACTAGTTGTTTTAAGAAATGTGGTGGTTGTTGTGATGATTATACTGGATACCAGGAGTTAGTAATCAAAACTTCACATGACGACTAA
Protein
MFLILLISLPTAFAVIGDLNCTLDPRLKGSFNNRDTGHPSISTDTVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGSTYRNMALKGTDLLSTLWFKPPFLSDFINGIFAKVKNTKVFIDGVMYSEFPAITIGSTFVNTSYSVVVQPRTINSTQDGVNKLQGLLEVSVCQYNMCEYPHTICHPNLGNHFKELWHYDTGVVSCLYKRNFTYDVNATYLYFHFYQEGGTFYAYFTDTGFVTKFLFNVYLGMALSHYYVMPLTCIRRAKHGFSLEYWVTPLTPRQYLLAFNQDGIIFNAVDCMSDFMSEIKCKTQSIAPPTGVYELNGYTVQPIADVYRRKPDLPNCNIEAWLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNIDAAKIYGMCFSSITIDKFAIPNRRKVDLQLGNLGYLQSSNYRIDTTATSCQLYYNLPAANVSVSRFNPSTWNKRFGFIEDSVFVPQPTGVFTNHSVVYAQHCFKAPKNFCPCSSCPSKNNGIGTCPAGTNSLTCDNLCTLDPITLKAPDTYKCPQSKSLVGIGEHCSGLAVKSDYCGNNSCTCQPQAFLGWSADSCLQGDKCNIFANFILHDVNNGLTCSTDLQKANTEIELGVCVNYDLYGISGQGIFVEVNATYYNSWQNLLYDSNGNLYGFRDYITNRTFMIHSCYSGRVSAAYHANSSEPALLFRNIKCNYVFNNSLTRQLQPINYSFDSYLGCVVNAYNSTAISVQTCDLTVGSGYCVDYSKNRRSRRAITTGYRFTNFEPFTVNSVNDSLEPVGGLYEIQIPSEFTIGNMEEFIQTSSPKVTIDCAAFVCGDYAACKLQLVEYGSFCDNINAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNFNVDDINFSPVLGCLGSECSKASSRSAIEDLLFDKVKLSDVGFVEAYNNCTGGAEIRDLICVQSYKGIKVLPPLLSENQISGYTLAATSASLFPPWTAAAGVPFYLNVQYRINGLGVTMDVLSQNQKLIANAFNNALHAIQQGFDATNSALVKIQAVVNANAEALNNLLQQLSNRFGAISASLQEILSRLDALEAEAQIDRLINGRLTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKSQSSRINFCGNGNHIISLVQNAPYGLYFIHFNYVPTKYVTAKVSPGLCIAGNRGIAPKSGYFVNVNNTWMYTGSGYYYPEPITENNVVVMSTCAVNYTKAPYVMLNTSIPNLPDFKGELDQWFKNQTSVAPDLSLDYINVTFLDLQVEMNRLQEAIKVLNHSYINLKDIGTYEYYVKWPWYVWLLICLAGVAMLVLLFFICCCTGCGTSCFKKCGGCCDDYTGYQELVIKTSHDD
Summary
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.
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.
Similarity
Belongs to the betacoronaviruses spike protein family.
Feature
chain Spike protein S2
Uniprot
Pubmed
Proteomes
Interpro
SUPFAM
SSF143587
SSF143587
Gene 3D
ProteinModelPortal
PDB
6OHW
E-value=0.0 Score=2352 Identity=91.98%
Cov(Q)=94.62% Cov(P)=97.20%
3D Structure
Ontologies
GO
GO:0039654 P:fusion of virus membrane with host endosome membrane
GO:0046813 P:receptor-mediated virion attachment to host cell
GO:0044173 C:host cell endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0009405 P:pathogenesis
GO:0075509 P:endocytosis involved in viral entry into host cell
GO:0016021 C:integral component of membrane
GO:0019031 C:viral envelope
GO:0019064 P:fusion of virus membrane with host plasma membrane
GO:0055036 C:virion membrane
GO:0020002 C:host cell plasma membrane
GO:0046813 P:receptor-mediated virion attachment to host cell
GO:0044173 C:host cell endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0009405 P:pathogenesis
GO:0075509 P:endocytosis involved in viral entry into host cell
GO:0016021 C:integral component of membrane
GO:0019031 C:viral envelope
GO:0019064 P:fusion of virus membrane with host plasma membrane
GO:0055036 C:virion membrane
GO:0020002 C:host cell plasma membrane
Subcellular Location
From MSLVP
Host nucleus > host nucleolus. Host cytoplasm. Secreted.
From Uniprot
Virion membrane
Accumulates in the endoplasmic reticulum-Golgi intermediate compartment, where it participates in virus particle assembly. Some S oligomers are transported to the host plasma membrane, where they may mediate cell-cell fusion. With evidence from 1 publications.
Host endoplasmic reticulum-Golgi intermediate compartment membrane Accumulates in the endoplasmic reticulum-Golgi intermediate compartment, where it participates in virus particle assembly. Some S oligomers are transported to the host plasma membrane, where they may mediate cell-cell fusion. With evidence from 1 publications.
Host cell membrane Accumulates in the endoplasmic reticulum-Golgi intermediate compartment, where it participates in virus particle assembly. Some S oligomers are transported to the host plasma membrane, where they may mediate cell-cell fusion. With evidence from 1 publications.
Host endoplasmic reticulum-Golgi intermediate compartment membrane Accumulates in the endoplasmic reticulum-Golgi intermediate compartment, where it participates in virus particle assembly. Some S oligomers are transported to the host plasma membrane, where they may mediate cell-cell fusion. With evidence from 1 publications.
Host cell membrane Accumulates in the endoplasmic reticulum-Golgi intermediate compartment, where it participates in virus particle assembly. Some S oligomers are transported to the host plasma membrane, where they may mediate cell-cell fusion. With evidence from 1 publications.
Topology
Length:
1358
Number of predicted TMHs:
1
Exp number of AAs in TMHs:
26.90384
Exp number, first 60 AAs:
0.83381
Total prob of N-in:
0.03666
outside
1 - 1302
TMhelix
1303 - 1325
inside
1326 - 1358
