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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)
Scope(s) Viruses
Template(s) P59594 (SPIKE_SARS); [ Recover all ]
Triggered by HAMAP; MF_04099 (Get profile general information and statistics)

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;
RecName: Full=Spike protein S1;
RecName: Full=Spike protein S2;
RecName: Full=Spike protein S2';
                 Flags: Precursor;
Gene name Name=S;

Comments [?]

FUNCTIONSpike protein S1: attaches the virion to the cell membrane by interacting with host receptor, initiating the infection.
FUNCTIONSpike 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.
FUNCTIONSpike protein S2': Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.
SUBUNITHomotrimer; each monomer consists of a S1 and a S2 subunit. The resulting peplomers protrude from the virus surface as spikes.
SUBCELLULAR LOCATIONVirion 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.
DOMAINFusion 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.
PTMSpecific 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.
PTMThe cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes.
SIMILARITYBelongs 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 [?]

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 [?]

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 [?]

Size range 1235-1376 amino acids
Related rules None
Fusion Nter: None Cter: None

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