HAMAP rule MF_04098
General rule information
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| Accession | MF_04098 |
| Dates | 26-MAR-2018 (Created)
29-SEP-2022 (Last updated, Version 6) |
| Name | GAMMA_CORONA_SPIKE |
| Scope(s) |
Viruses Gammacoronavirus |
| Template(s) | P11223 (SPIKE_IBVB); [ Recover all ] |
| Triggered by |
HAMAP; MF_04098 (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 host cell membrane by interacting with sialic acids, 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 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. |
| FUNCTION | Spike protein S2': 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. |
| SUBCELLULAR LOCATION | Spike protein S2: Virion membrane; Single-pass type I membrane protein. Host endoplasmic reticulum-Golgi intermediate compartment 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 may be transported to the plasma membrane, where they may mediate cell-cell fusion. |
| SUBCELLULAR LOCATION | Spike protein S1: Virion membrane; Peripheral membrane protein. Host endoplasmic reticulum-Golgi intermediate compartment membrane; Peripheral membrane protein. Note=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. S1 is not anchored to the viral envelope, but associates with the extravirion surface through its binding to S2. |
| case <FTTag:Motif> | |
| DOMAIN | The di-lysine motif confers endoplasmic reticulum localization for type I membrane proteins. |
| end case | |
| PTM | Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host cell furin or furin-like protease to yield the mature S1 and S2 proteins. The cleavage site between S1 and S2 requires the optimal sequence [KR]-X-[KR]-R. Additionally, a second cleavage leads to the release of a fusion peptide after viral attachment to host cell receptor. |
| SIMILARITY | Belongs to the gammacoronaviruses 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 | PF01600; Corona_S1; 1; |
| Pfam | PF01601; Corona_S2; 1; |
| General | Coiled_coil; -; 2-unlimited; |
| General | Signal; -; 1; |
| General | Transmembrane; -; 1; |
Features
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| From: SPIKE_IBVB (P11223) | ||||||||||||
| Key | From | To | Description | Tag | Condition | FTGroup | ||||||
| SIGNAL | Nter | 18 | ||||||||||
| CHAIN | 19 | 537 | /note="Spike protein S1" | |||||||||
| CHAIN | 538 | Cter | /note="Spike protein S2" | |||||||||
| CHAIN | 691 | Cter | /note="Spike protein S2'" | |||||||||
| TOPO_DOM | 19 | 1095 | /note="Extracellular" | |||||||||
| TRANSMEM | 1096 | 1116 | /note="Helical" | |||||||||
| TOPO_DOM | 1117 | Cter | /note="Cytoplasmic" | |||||||||
| COILED | 822 | 866 | ||||||||||
| COILED | 1055 | 1083 | ||||||||||
| MOTIF | 1159 | 1162 | /note="Di-lysine motif" | Motif | K-K-x-x | |||||||
| SITE | 537 | 538 | /note="Cleavage; by host furin" | R-S | ||||||||
| SITE | 690 | 691 | /note="Cleavage; by host furin" | R-S | ||||||||
Additional information
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| Size range | 1154-1163 amino acids |
| Related rules |
None |
| Fusion | Nter: None Cter: None |