Strain
Deer_FJ425189
(Region: USA: Ohio; Strain: Sambar deer coronavirus US/OH-WD388/1994, complete genome.; Date: 1-Jan-94)
Gene
spike protein
Description
Annotated in NCBI,
spike protein
Location
GenBank Accession
Full name
Spike glycoprotein
Alternative Name
E2
Peplomer protein
Peplomer protein
Sequence
CDS
ATGTTTTTGATACTTTTAATTTCCTTACCAACGGCTTTTGCTGTTATAGGAGATTTAAAGTGTACTACAGTTTCCATTAATGATGTTGACACTGGTGTTCCTTCTATTAGCACTGATACTGTCGATGTTACTAATGGTTTAGGTACTTATTATGTTTTAGATCGTGTGTATTTAAATACTACGTTGTTGCTTAATGGTTACTACCCTACTTCAGGTTCTACATATCGTAATATGGCACTGAAGGGAACTTTACTATTGAGCACACTATGGTTTAAACCACCTTTTCTTTCTGATTTTACTAATGGTATTTTTGCTAAGGTCAAAAATACCAAGGTTATTAAAGATGGTGTAATGTATAGTGAGTTTCCTGCTATAACTATAGGTAGTACTTTTGTAAATACATCCTATAGTGTGGTAGTACAACCACATACTACTAATTTGGATAATAAATTACAAGGTTTCTTAGAGATCTCTGTTTGCCAGTATACTATGTGCGAGTACCCAAATACGATTTGTAATCCTAATCTGGGTAACCAACGCGTAGAATTATGGCATTGGGATACAGGTGTTGTTTCCTGTTTATATAAGCGTAATTTCACATATGATGTGAATGCTGATTATTTGTATTTTCATTTTTATCAAGAAGGTGGTACTTTTTATGCATATTTTACAGACACTGGTGTTGTTACTAAGTTTCTGTTTAATGTTTATTTAGGCACGGTGCTCTCACATTATTATGTCATGCCTTTGACTTGTAATAGTGCTCTGACTTTAGAATATTGGGTTACACCCCTCACTTCTAAACAATATCTACTAGCTTTCAATCAAGACGGTGTTATTTTTAATGCTGTTGATTGTAAGAGTGATTTTATGAGTGAGATTAAGTGTAAAACACTATCTATAGCACCATCTACTGGTGTTTATGAATTAAACGGTTACACTGTTCAGCCAATTGCAGATGTTTACCGACGTATACCTAATCTTCCCGATTGCAATATTGAGGCTTGGCTTAATGATAAGTCGGTGCCCTCTCCATTAAATTGGGAACGTAAGACCTTTTCAAATTGTAATTTTAATATGAGCAGCCTGATGTCTTTTATTCAGGCAGACTCATTTACTTGTAATAATATTGATGCTGCTAAGATATATGGTATGTGTTTTTCCAGCATAACTATAGATAAGTTTGCAATACCCAATGGTAGGAAGGTTGACCTACAATTGGGTAATTTGGGCTATTTGCAGTCTTTTAACTATAGAATTGATACTACTGCTACAAGTTGTCAGTTGTATTATAATTTACCTGCTGCTAATGTTTCTGTTAGCAGGTTTAATCCTTCTACTTGGAATAGGAGATTTGGTTTTACAGAACAATCTGTTTTTAAGCCTCAACCTGCAGGTGTTTTTACTGATCATGATGTTGTTTATGCACAACATTGTTTTAAAGCTCCCACAAATTTCTGTCCGTGTAAATTGGATGGGTCTTTGTGTGTAGGTAGTGGTTCTGGTATAGATGCTGGTTATAAAAATACTGGTATAGGCACTTGTCCTGCAGGTACTAATTATTTAACTTGTCATAATGCTGCCCAATGTGATTGTTTGTGCACTCCAGACCCCATTACATCTAAAGCTACAGGGCCTTACAAGTGCCCCCAAACTAAATATTTAGTTGGTATAGGTGAGCACTGTTCGGGTCTTGCTATTAAAAGTGATCATTGTGGAGGTAATCCTTGTACTTGCCAACCACAAGCATTTTTGGGTTGGTCTGTTGACTCTTGTTTACAAGGGGATAGGTGTAATATTTTTGCTAATTTTATTTTGCATGATGTTAATAGTGGTACTACTTGTTCTACTGATTTACAAAAATCAAACACAGACATAATTCTTGGTGTTTGTGTTAATTATGATCTTTATGGTATTACTGGCCAAGGTATTTTTGTTGAGGTTAATGCGACTTATTATAATAGTTGGCAGAACCTTTTATATGATTCTAATGGTAATCTCTATGGTTTTAGAGACTACTTAACAAATAGAACTTTTATGATTCGTAGTTGCTATAGCGGTCGTGTTTCAGCGGCCTTTCATGCTAACTCTTCCGAACCAGCATTGCTATTTCGGAATATTAAATGCAATTACGTTTTTAATAATACTCTTTCACGACAGCTGCAACCTATTAACTATTTTGATAGCTATCTTGGTTGTGTTGTCAATGCTGATAATAGTACTTCTAGTGTTGTTCAAACATGTGATCTCACAGTAGGTAGTGGTTACTGTGTGGATTACTCTACAAAAAGACGAAGTCGTAGATCGATTACCACTGGTTATCGGTTTACTAATTTTGAGCCATTTACTGTTAATTCAGTAAATGATAGTTTAGAACCTGTAGGTGGTTTGTATGAAATTCAAATACCTTCAGAGTTTACTATAGGTAATATGGAGGAGTTTATTCAAACAAGCTCTCCTAAAGTTACTATTGATTGTTCTGCTTTTGTCTGTGGTGATTATGCAGCATGTAAATCACAGTTGGTTGAATATGGTAGCTTCTGTGACAATATTAATGCTATACTCACAGAAGTAAATGAACTACTTGACACTACACAGTTGCAAGTAGCTAATAGTTTAATGAATGGTGTCACTCTTAGCACTAAGCTTAAAGATGGCGTTAATTTCAATGTAGACGACATCAATTTTTCCCCTGTATTAGGTTGTTTAGGAAGCGATTGTAATAAAGTTTCCAGTAGATCTGCTATAGAGGATTTACTTTTTTCTAAAGTAAAGTTATCTGATGTCGGTTTTGTTGAGGCTTATAATAATTGTACTGGAGGCGCCGAAATTAGGGACCTCATTTGTGTGCAAAGTTATAATGGTATCAAGGTGTTGCCTCCACTGCTCTCAGAAAATCAGATCAGTGGATACACTTTGGCTGCCACCTCTGCTAGTCTGTTTCCTCCTTGGTCAGCAGCAGCAGGTGTACCATTTTATTTAAATGTTCAGTATCGTATTAATGGGATTGGTGTTACCATGGATGTGCTAAGTCAAAATCAAAAGCTTATTGCTAATGCATTTAACAATGCTCTTGGTGCTATTCAGGAAGGGTTTGATGCTACCAATTCTGCTTTAGTTAAAATTCAATCTGTTGTTAATGCAAATGCTGAAGCTCTTAATAACTTATTGCAACAACTCTCTAATAGATTTGGTGCTATAAGTTCTTCTTTACAAGAAATTCTATCTAGACTGGATGCTCTTGAAGCGCAAGCTCAGATAGACAGACTTATTAATGGGCGTCTTACCGCTCTTAATGCTTATGTTTCTCAACAGCTTAGTGACTCTACACTAGTAAAGTTTAGTGCAGCACAAGCTATGGAGAAGGTTAATGAATGTGTCAAAAGCCAATCATCTAGGATAAATTTTTGTGGTAATGGTAATCATATTATATCATTAGTGCAGAATGCTCCATATGGTTTGTATTTTATCCACTTTAGCTATGTCCCTACCAAGTATGTCACTGCGAAGGTTAGTCCCGGTCTGTGCATTGCTGGTGATAGAGGTATAGCCCCTAAGAGTGGTTATTTTGTTAATGTAAATAATACTTGGATGTTCACTGGTAGTGGTTATTACTACCCTGAACCTATAACTGGAAATAATGTTGTTGTTATGAGTACCTGTGCTGTTAATTATACTAAAGCGCCGGATGTAATGCTGAACATTTCAACACCCAACCTCCCTGATTTTAAGGAAGAGTTGGATCAATGGTTTAAAAACCAAACATCAGTGGCACCAGATTTGTCACTTGATTATATAAATGTTACATTCTTGGACCTACAAGATGAAATGAATAGGTTACAGGAGGCAATAAAAGTTTTAAATCAGAGCTACATCAATCTCAAGGACATTGGTACATATGAGTATTATGTAAAATGGCCTTGGTATGTATGGCTTTTAATTGGCTTTGCTGGTGTAGCTATGCTTGTTTTACTATTCTTCATATGCTGTTGTACAGGATGTGGGACTAGTTGTTTTAAGAAATGTGGTGGTTGTTGTGATGATTATACTGGACACCAGGAGTTAGTAATTAAAACATCACATGACGACTAA
Protein
MFLILLISLPTAFAVIGDLKCTTVSINDVDTGVPSISTDTVDVTNGLGTYYVLDRVYLNTTLLLNGYYPTSGSTYRNMALKGTLLLSTLWFKPPFLSDFTNGIFAKVKNTKVIKDGVMYSEFPAITIGSTFVNTSYSVVVQPHTTNLDNKLQGFLEISVCQYTMCEYPNTICNPNLGNQRVELWHWDTGVVSCLYKRNFTYDVNADYLYFHFYQEGGTFYAYFTDTGVVTKFLFNVYLGTVLSHYYVMPLTCNSALTLEYWVTPLTSKQYLLAFNQDGVIFNAVDCKSDFMSEIKCKTLSIAPSTGVYELNGYTVQPIADVYRRIPNLPDCNIEAWLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNIDAAKIYGMCFSSITIDKFAIPNGRKVDLQLGNLGYLQSFNYRIDTTATSCQLYYNLPAANVSVSRFNPSTWNRRFGFTEQSVFKPQPAGVFTDHDVVYAQHCFKAPTNFCPCKLDGSLCVGSGSGIDAGYKNTGIGTCPAGTNYLTCHNAAQCDCLCTPDPITSKATGPYKCPQTKYLVGIGEHCSGLAIKSDHCGGNPCTCQPQAFLGWSVDSCLQGDRCNIFANFILHDVNSGTTCSTDLQKSNTDIILGVCVNYDLYGITGQGIFVEVNATYYNSWQNLLYDSNGNLYGFRDYLTNRTFMIRSCYSGRVSAAFHANSSEPALLFRNIKCNYVFNNTLSRQLQPINYFDSYLGCVVNADNSTSSVVQTCDLTVGSGYCVDYSTKRRSRRSITTGYRFTNFEPFTVNSVNDSLEPVGGLYEIQIPSEFTIGNMEEFIQTSSPKVTIDCSAFVCGDYAACKSQLVEYGSFCDNINAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNFNVDDINFSPVLGCLGSDCNKVSSRSAIEDLLFSKVKLSDVGFVEAYNNCTGGAEIRDLICVQSYNGIKVLPPLLSENQISGYTLAATSASLFPPWSAAAGVPFYLNVQYRINGIGVTMDVLSQNQKLIANAFNNALGAIQEGFDATNSALVKIQSVVNANAEALNNLLQQLSNRFGAISSSLQEILSRLDALEAQAQIDRLINGRLTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKSQSSRINFCGNGNHIISLVQNAPYGLYFIHFSYVPTKYVTAKVSPGLCIAGDRGIAPKSGYFVNVNNTWMFTGSGYYYPEPITGNNVVVMSTCAVNYTKAPDVMLNISTPNLPDFKEELDQWFKNQTSVAPDLSLDYINVTFLDLQDEMNRLQEAIKVLNQSYINLKDIGTYEYYVKWPWYVWLLIGFAGVAMLVLLFFICCCTGCGTSCFKKCGGCCDDYTGHQELVIKTSHDD
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
EMBL
Interpro
SUPFAM
SSF143587
SSF143587
Gene 3D
ProteinModelPortal
PDB
6OHW
E-value=0.0 Score=2298 Identity=88.90%
Cov(Q)=95.82% Cov(P)=98.79%
3D Structure
Ontologies
GO
GO:0020002 C:host cell plasma membrane
GO:0055036 C:virion membrane
GO:0019064 P:fusion of virus membrane with host plasma membrane
GO:0019031 C:viral envelope
GO:0009405 P:pathogenesis
GO:0016021 C:integral component of membrane
GO:0075509 P:endocytosis involved in viral entry into host cell
GO:0044173 C:host cell endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0046813 P:receptor-mediated virion attachment to host cell
GO:0039654 P:fusion of virus membrane with host endosome membrane
GO:0055036 C:virion membrane
GO:0019064 P:fusion of virus membrane with host plasma membrane
GO:0019031 C:viral envelope
GO:0009405 P:pathogenesis
GO:0016021 C:integral component of membrane
GO:0075509 P:endocytosis involved in viral entry into host cell
GO:0044173 C:host cell endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0046813 P:receptor-mediated virion attachment to host cell
GO:0039654 P:fusion of virus membrane with host endosome 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:
1363
Number of predicted TMHs:
1
Exp number of AAs in TMHs:
23.74553
Exp number, first 60 AAs:
0.11147
Total prob of N-in:
0.00631
outside
1 - 1307
TMhelix
1308 - 1330
inside
1331 - 1363
