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HAMAP rule MF_04099

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General rule information [?]

Accession MF_04099
Dates 20-MAR-2018 (Created)
29-SEP-2022 (Last updated, Version 10)
Viruses; Betacoronavirus
Template P59594 (SPIKE_SARS)

Propagated annotation [?]

Identifier, protein and gene names [?]

Protein name
RecName: Full=Spike glycoprotein;
Short=S glycoprotein;
AltName: Full=E2;
AltName: Full=Peplomer protein;
RecName: Full=Spike protein S1;
RecName: Full=Spike protein S2;
RecName: Full=Spike protein S2';
Flags: Precursor;
Gene name

Comments [?]

Function Spike protein S1: attaches the virion to the cell membrane by interacting with host receptor, 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 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.
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.
The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes.
Similarity Belongs to the betacoronaviruses spike protein family.

Keywords [?]

Gene Ontology [?]

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 [?]

PROSITE PS00001; ASN_GLYCOSYLATION; 0-unlimited; trigger=PRU00498;
Pfam PF01601; Corona_S2; 1;
PF16451; Spike_NTD; 1;
PF09408; Spike_rec_bind; 1;

Computed features [?]

General Coiled_coil; -; 0-unlimited;
Signal; -; 1;
Transmembrane; -; 1;

Features [?]

From: SPIKE_SARS (P59594)
Key     From     To       Description   Tag   Condition   FTGroup
SIGNAL     Nter     13                
CHAIN     14     667       Spike protein S1        
CHAIN     668     Cter       Spike protein S2        
CHAIN     798     Cter       Spike protein S2'        
TOPO_DOM     14     1195       Extracellular        
TRANSMEM     1196     1216       Helical        
TOPO_DOM     1217     Cter       Cytoplasmic        
REGION     798     819       Fusion peptide 1        
REGION     817     837       Fusion peptide 2        
REGION     902     952       Heptad repeat 1        
REGION     1145     1184       Heptad repeat 2        
COILED     931     975                
COILED     1157     1185                
MOTIF     1251     Cter       KxHxx        
SITE     667     668       Cleavage     R-S  
SITE     797     798       Cleavage     R-S  
DISULFID     323     348             C-x*-C  
DISULFID     366     419             C-x*-C  
DISULFID     822     833             C-x*-C  
SITE     760     761       Cleavage     R-S  

Additional information [?]

Size range 1235-1376 amino acids
Related rules None
Fusion None