Full-length SwissProt precursor protein sequences (before cleavage into protein products) (P0DTC2)
 
Item: P0DTC2
Score: 1000
Position: NC_045512v2:21563-25381
Genomic Size: 3819
Strand: +
View DNA for this feature (wuhCor1/SARS-CoV-2)

Alternative/human readable name
Status of CDS start annotation (none, unknown, incomplete, or complete)cmpl
Status of CDS end annotation (none, unknown, incomplete, or complete)cmpl
Exon frame {0,1,2}, or -1 if no frame for exon0
Transcript typeswissprot
Primary identifier for gene
Alternative/human-readable gene name
Gene type
UniProt main accessionP0DTC2
UniProt main record nameSPIKE_SARS2
UniProt statusManually reviewed (Swiss-Prot)
UniProt all accessionsP0DTC2
UniProt isoform accessions
UniProt protein nameSpike glycoprotein
UniProt protein short nameS glycoprotein
UniProt alternative namesE2; Peplomer protein
UniProt alternative short names
UniProt gene nameS
UniProt gene synonymsORF2
UniProt function
  • Molecule 'Spike protein S1': attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Binding to host NRP1 and NRP2 via C-terminal polybasic sequence enhances virion entry into host cell (PubMed:33082294, PubMed:33082293). This interaction may explain virus tropism of human olfactory epithelium cells, which express high level of NRP1 and NRP2 but low level of ACE2 (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Uses human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Can be alternatively processed by host furin (PubMed:32362314). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.
  • Molecule '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.
  • Molecule 'Spike protein S2'': Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.
  • Molecule 'Spike glycoprotein': May down-regulate host tetherin (BST2) by lysosomal degradation, thereby counteracting its antiviral activity.
HGNC Gene Symbol
HGNC ID
RefSeq IDsNC_045512.2
RefSeq Protein IDsYP_009724390.1
NCBI Entrez Gene43740568
Ensembl Gene IDs
Ensembl Transcript IDs
Ensembl Protein IDs

Links to sequence:

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Source data version: UniProt Covid-19 pre-release 28-Apr-2021
Data last updated at UCSC: 2021-03-22 05:38:39

Description

This track shows protein sequence annotations from the UniProt/SwissProt database, mapped to genomic coordinates. The data has been curated from scientific publications by the UniProt/SwissProt staff. The annotations are spread over multiple tracks, based on their "feature type" in UniProt:

Track Name Description
UCSC Alignment, SwissProt Protein sequences from SwissProt mapped onto the genome. All other tracks are (start,end) annotations mapped using this track.
UCSC Alignment, TrEMBL Protein sequences from TrEMBL mapped onto the genome. All other tracks are (start,end) annotations mapped using this track. This track is hidden by default. To show it, click its checkbox on the track description page.
UniProt Signal Peptides Regions found in proteins destined to be secreted, generally cleaved from mature protein.
UniProt Extracellular Domains Protein domains with the comment "Extracellular".
UniProt Transmembrane Domains Protein domains of the type "Transmembrane".
UniProt Cytoplasmic Domains Protein domains with the comment "Cytoplasmic".
UniProt Polypeptide Chains Polypeptide chain in mature protein after post-processing.
UniProt Domains Protein domains, zinc finger regions and topological domains.
UniProt Disulfide Bonds Disulfide bonds.
UniProt Amino Acid Modifications Glycosylation sites, modified residues and lipid moiety-binding regions.
UniProt Amino Acid Mutations Mutagenesis sites and sequence variants.
UniProt Protein Primary/Secondary Structure Annotations Beta strands, helices, coiled-coil regions and turns.
UniProt Sequence Conflicts Differences between Genbank sequences and the UniProt sequence.
UniProt Repeats Regions of repeated sequence motifs or repeated domains.
UniProt Other Annotations All other annotations

Display Conventions and Configuration

Genomic locations of UniProt/SwissProt annotations are labeled with a short name for the type of annotation (e.g. "glyco", "disulf bond", "Signal peptide" etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt record for more details. TrEMBL annotations are always shown in light blue, except in the Signal Peptides, Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.

Mouse-over a feature to see the full UniProt annotation comment. For variants, the mouse-over will show the full name of the UniProt disease acronym.

The subtracks for domains related to subcellular location are sorted from outside to inside of the cell: Signal peptide, extracellular, transmembrane, and cytoplasmic.

In the "UniProt Modifications" track, lipoification sites are highlighted in dark blue, glycosylation sites in dark green, and phosphorylation in light green.

Methods

UniProt sequences were aligned to UCSC/Gencode transcript sequences first with BLAT, filtered with pslReps (93% query coverage, within top 1% score), lifted to genome positions with pslMap and filtered again. UniProt annotations were obtained from the UniProt XML file. The annotations were then mapped to the genome through the alignment using the pslMap program. This mapping approach draws heavily on the LS-SNP pipeline by Mark Diekhans. Like all Genome Browser source code, the main script used to build this track can be found on GitHub.

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server. The exact filenames can be found in the track configuration file. Annotations can be converted to ASCII text by our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example:

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/uniprot/unipStructCov2.bb -chrom=NC_045512v2 -start=0 -end=29903 stdout

Please refer to our mailing list archives for questions or our Data Access FAQ for more information.

Credits

This track was created by Maximilian Haeussler at UCSC, with help from Chris Lee, Mark Diekhans and Brian Raney, feedback from the UniProt staff and Phil Berman, UCSC. Thanks to UniProt for making all data available for download.

References

UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5. PMID: 22102590; PMC: PMC3245120

Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants. Hum Mutat. 2004 May;23(5):464-70. PMID: 15108278