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Annotation rule MF_04098
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General rule information [?]

Accession MF_04098
Dates 26-MAR-2018 (Created)
20-NOV-2019 (Last updated, Version 5)
Name GAMMA_CORONA_SPIKE
Scope
Viruses; Gammacoronavirus
Template P11223 (SPIKE_IBVB)
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

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
S

Comments [?]

Function Spike protein S1: attaches the virion to the host cell membrane by interacting with sialic acids, initiating the infection.
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.
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.
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 [?]

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

Gene Ontology [?]

GO:0044173; Cellular component: host cell endoplasmic reticulum-Golgi intermediate compartment membrane.
GO:0016021; Cellular component: integral component of 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 [?]

PROSITE PS00001; ASN_GLYCOSYLATION; 0-unlimited; trigger=PRU00498;
Pfam PF01600; Corona_S1; 1;
PF01601; Corona_S2; 1;

Computed features [?]

General Coiled_coil; -; 2-unlimited; trigger=yes;
Signal; -; 1;
Transmembrane; -; 1;

Features [?]

From: SPIKE_IBVB (P11223)
Key     From     To       Description   Tag   Condition   FTGroup
SIGNAL     Nter     18                
CHAIN     19     537       Spike protein S1        
CHAIN     538     Cter       Spike protein S2        
CHAIN     691     Cter       Spike protein S2'        
TOPO_DOM     19     1095       Extracellular        
TRANSMEM     1096     1116       Helical        
TOPO_DOM     1117     Cter       Cytoplasmic        
COILED     822     866                
COILED     1055     1083                
MOTIF     1159     1162       Di-lysine motif   Motif   K-K-x-x  
SITE     537     538       Cleavage; by host furin     R-S  
SITE     690     691       Cleavage; by host furin     R-S  

Additional information [?]

Size range 1154-1163 amino acids
Related rules None
Fusion None


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