Strain
Avian_KM454473
(Region: China; Strain: Duck coronavirus isolate DK/GD/27/2014, complete genome.; Date: 2014)
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
ATGTTGGCAACGTTAGTTTTGTTGACGACAGTTTTGTGTGTTGCTAATCCATGTTTAACTTTTAATGGTACTTCTCATGGTGTACATGATGGTAATTTCACTGCACGTGTTTGTGATGGGCCTGCTGGTTATTATTCTTCATCACCAATTCGTCCATCTGACGGTGTCTATAGTGTTAACGGTTTTTATAAACCCGTTTATACATGTTGTATAAGGCATACCTATCCGAAAAATACGACGCAGTGTGCGAATAAAAAAGTTTCTGTTTTGTATTATATTAACGACACAACAGAGGCTTTTTCCATTACCATACCCAGAGCCGTTGTTATTAAACCGGACACAGAATCTTTCATTTTGTCGCTGGGTGATTTTTTACTCACAGCTAAACAGCTGTTAGTTTATGGCACTATTCAGTCTCTTATGTTTTTGCGTAATGGTACTTGGTATATTAACGGTGTTCCGGCTCTTCCTGTCAGTTACACCTTTAATACCACTTTAAATGTCACTCATACTAGCTGTTATGAGAGTATTGGTGCACAAACTTTTTATTTTACTTCACTAATCCTTTCTAATGGGTTAGTTGAATTTTCTGCTGGCAACCTTCTTCGGTCTGTTGCTTGTGAAGACAACACTATTATAAACTCTATGCAATGTAGTCACCAGCGATTTAATTTTTCGACTGGTTTGCATTCTTATGACAGTGTTGTTCCTGTTTCTGGTAATGTCACCTACATTCCTTACCCTGGTGTCGGGGACAATTCGAGTTTGGAGTTGTACAGTCTTAATGTTTCGCTTCGTTCTAAAGGTAACTATGGCGTTCATTATAACTATACTTGTGTTAATGCTTCTCTGTACACCTATTTTCGTGTTTATTGTCAGGATGAACATGATTGGAATACAGAAAAGCTATGTACTGTGTCTGACTATTATGTGCCTGGTAGACATTTGTATGGCAGCCAACATCAATATGTTGGCATTGTCCCTCATTATACTACCTGTTCTTCGTTAGGGCTTAGCCTTAGTAATATTAATAATAATTTGGGTTTTGATACTTTTTGTATTACTAATGCTAGGTCTACTTATAATATAGCAGAAGTCACCCAGTTTCAATGTCTTTTTGTGATTGATGTTATGGTTTTTGATGCTACAGGTGGTAGTAGTTGGGGTCAACCTATTGAATATTTTTATGTTGGCCTCGATTTTTCTTTTGGTAATAGAATGTATGGTGTCTTGCAAATTCCTCCGCAAGTTATATATGAAGACCAGTGTCATTCTTATGATATTTATGGTATTAAAGGCACTGGTCACATCTATAATGTCACTGGTTATGACAATTACACCTTATCTACAGGTGGTTTGGCTATATCAGGTGGTAATGGTCTATTGGCCTTTCGTAATAATGGTTCTTTGTATACTGTCAAACCGTGTTCTACAGTATCTACTCAGGCTGTTATTGTAGCTAACCAGTTGGCAGGGTTGTATTTACCGCTCTCATGTGACATAGTTTTTAATCTTAATCTTGGTAATGAAACTACTCCTGTTGATGGCGGCTGTTTAGTTTTTAATTCAACTTTTAAGAACCGACAATCACAGCTTTATGGCAGTGAGTGTTATGGTGTATTTGCCACTATTGGTTCTTCGTGTATTTATGCTAATTCTTCTGTGTTAAATCGTACACTGCCGAGGGCAGGCGTAGATACCACTGTAGAACCATTATTGGATGTGACGGCCAATGTTTCCATACCCTATACCCTGACACTGGCGGTCACTACTGAATACTTACAAACATCTTACCAGAAAGTCACTATTGACTGTGCCCGGTATGTGTGTGGTGAGTCTCTTAAATGTCGTACTCTTTTGCAGCAGTATGGCAGTTTTTGTACCAGCGTTAATAATATATTAGCTGGTGTTAACGATAATGAGGATAACGGCATGCTTTCTTTTGTGGAGGCTATTAATACTGGTTATTCTCTTAACTTTTCTAGTTTTAACAGTTCAAACCTTGGTGGGTTTAATCTGTCGTTAGTCTTACCTAATTCAGCAAAGCCCTCGGGACGTTCCTTTATTGAAGATTTACTCTTTGATAAAGTGGTTACTGTCGGTGTGGGTGAAGTTGATGCTAATTATGATAAGTGCATGGATTCAAGAGGCGGCAAGTTTACTAATGCTGCTGACTTGACATGTGCTCAGTTTTATAATGGTATCATGGTGCTTCCTGGAGTGGTGGACCCAGACCTTATGACACTTTATACAGGCTCACTTCTGGGTGGCATGTCTTTTGGTGGTCTTTCTTCTGCTGCCTCTATACCTTTTGCCACACAGGTGCAGGCCCGTATTAATTATTTGGCACTTACTCAGTCTGTGCTTTTGGATAATCAAAACCTTATTGCTAATTCATTTAATAATGCTCTTGAAAAAATACAGTCAGCACTTGATGTGGTGTCAGCTGGTTTTCAAGAGGTTGCAAAAGGCTTTGAGACTGTTTCTGTAGCACTTTCTAAGGTTCAGGATGTTGTTAATTCACATTCTGAGATTTTGAATAAACTTATGGCGCAGCTTAATGTTAATTTTGGCGCCATCTCTTCTTCTTTGTCTGATATCTATTCTCAACTTGACGAGCTTAATGCTAACGCTCAAGTTGATAGATTGATAACAGGTAGGTTGACAGCACTCTCTACATATGCAGCTTCTTTACAGTTGGCTGCATATAAAGCAGAAGAGTCGCGTAAATTGGCTTTGCAGAAAGTTGAAGAATGTGTTAAATCACAGTCTATGCGTTATGGGTTTTGTGGTAATGGCAGTCATGTTTTAACCATACCACAAACAGCACCTAATGGTATGTTTTTTATACACTATACCTATCCCCCTGCCTCATATATAACTGTTGAGGCGGTACCAGGGTTGTGTGTTACCACACGTACTGGTTCTTATGGTGTTATGCCTAAAACTGGTAGTGGTATTATATTTAGGGCTAACGGCACGTTCTTTGTAACTGCCCGTACTCTTTATCAGCCCAAATTGCTTTCTTATTCAGACGTCGTTAATTTAACGTCGTGTGAAGCTAATTATTATAATGTTAGCCAAGATGAAACACCGTTTCAGCCTGAGCTACCTAGTTTTGATGATGAGTTCGATAATATATATACCGAACTCAACACTTCTAAAGACCTCATAGACTCAATCTATAAGGATTTTAATTATACCATCCCTATTCTTAATTTAGAGGATGATATATGTAGGTTGAACTCTTCTATTAATGCGCTGTGGAATTACAGCTCTATTATAGATGAGATCAATGCTGCGCTCAATGACACTTACATTAACCTGGAACAACTTAATAAGGTTACCAGGTACATTAAGTGGCCTTGGTACGTTTGGCTTGCTATAGGTTTTGCATGCCTTATTTTTGTGTTAATCCTATGCTGGATTTTCTTTATGACTGGTTGTTGCGGATGTTGCTGTGGTTGTTTTGGTATAATACCTCTTATGTACAAGTGCAGCAAAAAATCTTCGTATTACACCACCTTTGATGATGATGTCGTAGGTGAACAAATCAGACCTAAAAAGTTTGTTTAA
Protein
MLATLVLLTTVLCVANPCLTFNGTSHGVHDGNFTARVCDGPAGYYSSSPIRPSDGVYSVNGFYKPVYTCCIRHTYPKNTTQCANKKVSVLYYINDTTEAFSITIPRAVVIKPDTESFILSLGDFLLTAKQLLVYGTIQSLMFLRNGTWYINGVPALPVSYTFNTTLNVTHTSCYESIGAQTFYFTSLILSNGLVEFSAGNLLRSVACEDNTIINSMQCSHQRFNFSTGLHSYDSVVPVSGNVTYIPYPGVGDNSSLELYSLNVSLRSKGNYGVHYNYTCVNASLYTYFRVYCQDEHDWNTEKLCTVSDYYVPGRHLYGSQHQYVGIVPHYTTCSSLGLSLSNINNNLGFDTFCITNARSTYNIAEVTQFQCLFVIDVMVFDATGGSSWGQPIEYFYVGLDFSFGNRMYGVLQIPPQVIYEDQCHSYDIYGIKGTGHIYNVTGYDNYTLSTGGLAISGGNGLLAFRNNGSLYTVKPCSTVSTQAVIVANQLAGLYLPLSCDIVFNLNLGNETTPVDGGCLVFNSTFKNRQSQLYGSECYGVFATIGSSCIYANSSVLNRTLPRAGVDTTVEPLLDVTANVSIPYTLTLAVTTEYLQTSYQKVTIDCARYVCGESLKCRTLLQQYGSFCTSVNNILAGVNDNEDNGMLSFVEAINTGYSLNFSSFNSSNLGGFNLSLVLPNSAKPSGRSFIEDLLFDKVVTVGVGEVDANYDKCMDSRGGKFTNAADLTCAQFYNGIMVLPGVVDPDLMTLYTGSLLGGMSFGGLSSAASIPFATQVQARINYLALTQSVLLDNQNLIANSFNNALEKIQSALDVVSAGFQEVAKGFETVSVALSKVQDVVNSHSEILNKLMAQLNVNFGAISSSLSDIYSQLDELNANAQVDRLITGRLTALSTYAASLQLAAYKAEESRKLALQKVEECVKSQSMRYGFCGNGSHVLTIPQTAPNGMFFIHYTYPPASYITVEAVPGLCVTTRTGSYGVMPKTGSGIIFRANGTFFVTARTLYQPKLLSYSDVVNLTSCEANYYNVSQDETPFQPELPSFDDEFDNIYTELNTSKDLIDSIYKDFNYTIPILNLEDDICRLNSSINALWNYSSIIDEINAALNDTYINLEQLNKVTRYIKWPWYVWLAIGFACLIFVLILCWIFFMTGCCGCCCGCFGIIPLMYKCSKKSSYYTTFDDDVVGEQIRPKKFV
Summary
Function
attaches the virion to the host cell membrane by interacting with sialic acids, 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 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) 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 after S2 cleavage occurring upon virus endocytosis.
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 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) 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 after 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.
Similarity
Belongs to the gammacoronaviruses spike protein family.
Keywords
Cleavage on pair of basic residues
Coiled coil
Fusion of virus membrane with host endosomal membrane
Fusion of virus membrane with host membrane
Glycoprotein
Host membrane
Host-virus interaction
Membrane
Signal
Transmembrane
Transmembrane helix
Viral attachment to host cell
Viral envelope protein
Viral penetration into host cytoplasm
Virion
Virulence
Virus endocytosis by host
Virus entry into host cell
Feature
chain Spike glycoprotein
Uniprot
Pubmed
EMBL
Gene 3D
ProteinModelPortal
PDB
6CV0
E-value=7e-132 Score= 431 Identity=39.78%
Cov(Q)=59.95% Cov(P)=64.62%
3D Structure
Ontologies
GO
GO:0044173 C:host cell endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0019031 C:viral envelope
GO:0075509 P:endocytosis involved in viral entry into host cell
GO:0016021 C:integral component of membrane
GO:0055036 C:virion membrane
GO:0046813 P:receptor-mediated virion attachment to host cell
GO:0039654 P:fusion of virus membrane with host endosome membrane
GO:0009405 P:pathogenesis
GO:0019064 P:fusion of virus membrane with host plasma membrane
GO:0019031 C:viral envelope
GO:0075509 P:endocytosis involved in viral entry into host cell
GO:0016021 C:integral component of membrane
GO:0055036 C:virion membrane
GO:0046813 P:receptor-mediated virion attachment to host cell
GO:0039654 P:fusion of virus membrane with host endosome membrane
GO:0009405 P:pathogenesis
GO:0019064 P:fusion of virus membrane with host plasma membrane
Subcellular Location
From MSLVP
Capsid
From Uniprot
Virion membrane
Accumulates in the endoplasmic reticulum-Golgi intermediate compartment, where it participates in virus particle assembly. Some S oligomers may be transported to the 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 may be transported to the 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 may be transported to the plasma membrane, where they may mediate cell-cell fusion. With evidence from 1 publications.
Topology
Length:
1191
Number of predicted TMHs:
1
Exp number of AAs in TMHs:
34.97336
Exp number, first 60 AAs:
0.84602
Total prob of N-in:
0.03988
outside
1 - 1122
TMhelix
1123 - 1145
inside
1146 - 1191
