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HAMAP rule MF_04099
General rule information
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| Accession | MF_04099 |
| Dates | 20-MAR-2018 (Created)
29-SEP-2022 (Last updated, Version 10) |
| Name | BETA_CORONA_SPIKE |
| Scope(s) |
Viruses Betacoronavirus |
| Template(s) | P59594 (SPIKE_SARS); [ Recover all ] |
| Triggered by |
HAMAP; MF_04099 (Get profile general information and statistics) |
Propagated annotation
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Identifier, protein and gene names
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| Identifier | SPIKE |
| Protein name | RecName: Full=Spike glycoprotein; Short=S glycoprotein; AltName: Full=E2; AltName: Full=Peplomer protein; Contains: RecName: Full=Spike protein S1; Contains: RecName: Full=Spike protein S2; Contains: RecName: Full=Spike protein S2'; Flags: Precursor; |
| Gene name | Name=S; |
Comments
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| FUNCTION | Spike protein S1: attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. |
| FUNCTION | 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. |
| FUNCTION | Spike protein S2': 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. |
| SUBCELLULAR LOCATION | Virion membrane; Single-pass type I membrane protein. Host endoplasmic reticulum-Golgi intermediate compartment membrane; Single-pass type I membrane protein. Host cell membrane; Single-pass type I membrane protein. Note=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. |
| DOMAIN | Fusion peptide 1 (FP1) and fusion peptide 2 (FP2) function cooperatively and have a membrane-ordering effect on lipid headgroups and shallow hydrophobic regions of target bilayers. They are considered as two domains of an extended, bipartite FP. The membrane-ordering activity is calcium-dependent and also dependent on correct folding, which is maintained by an internal disulfide bond in FP2. |
| PTM | Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host cell furin or another cellular protease to yield the mature S1 and S2 proteins. Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor. |
| PTM | The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes. |
| SIMILARITY | Belongs to the betacoronaviruses spike protein family. |
Keywords
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Gene Ontology
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| GO:0044173; Cellular component:host cell endoplasmic reticulum-Golgi intermediate compartment membrane |
| GO:0016020; Cellular component:membrane |
| GO:0019031; Cellular component:viral envelope |
| GO:0055036; Cellular component:virion membrane |
| GO:0075509; Biological process:endocytosis involved in viral entry into host cell |
| GO:0039654; Biological process:fusion of virus membrane with host endosome membrane |
| GO:0019064; Biological process:fusion of virus membrane with host plasma membrane |
| GO:0046813; Biological process:receptor-mediated virion attachment to host cell |
Cross-references
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| PROSITE | PS00001; ASN_GLYCOSYLATION; 0-unlimited; |
| Pfam | PF01601; Corona_S2; 1; |
| Pfam | PF16451; Spike_NTD; 1; |
| Pfam | PF09408; Spike_rec_bind; 1; |
| General | Coiled_coil; -; 0-unlimited; |
| General | Signal; -; 1; |
| General | Transmembrane; -; 1; |
Features
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| From: SPIKE_SARS (P59594) | ||||||||||||
| Key | From | To | Description | Tag | Condition | FTGroup | ||||||
| SIGNAL | Nter | 13 | ||||||||||
| CHAIN | 14 | 667 | /note="Spike protein S1" | |||||||||
| CHAIN | 668 | Cter | /note="Spike protein S2" | |||||||||
| CHAIN | 798 | Cter | /note="Spike protein S2'" | |||||||||
| TOPO_DOM | 14 | 1195 | /note="Extracellular" | |||||||||
| TRANSMEM | 1196 | 1216 | /note="Helical" | |||||||||
| TOPO_DOM | 1217 | Cter | /note="Cytoplasmic" | |||||||||
| REGION | 798 | 819 | /note="Fusion peptide 1" | |||||||||
| REGION | 817 | 837 | /note="Fusion peptide 2" | |||||||||
| REGION | 902 | 952 | /note="Heptad repeat 1" | |||||||||
| REGION | 1145 | 1184 | /note="Heptad repeat 2" | |||||||||
| COILED | 931 | 975 | ||||||||||
| COILED | 1157 | 1185 | ||||||||||
| MOTIF | 1251 | Cter | /note="KxHxx" | |||||||||
| SITE | 667 | 668 | /note="Cleavage" | R-S | ||||||||
| SITE | 797 | 798 | /note="Cleavage" | R-S | ||||||||
| DISULFID | 323 | 348 | C-x*-C | |||||||||
| DISULFID | 366 | 419 | C-x*-C | |||||||||
| DISULFID | 822 | 833 | C-x*-C | |||||||||
| SITE | 760 | 761 | /note="Cleavage" | R-S | ||||||||
Additional information
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| Size range | 1235-1376 amino acids |
| Related rules |
None |
| Fusion | Nter: None Cter: None |