SARS-CoV-2 spike glycoprotein

SARS-CoV-2 spike glycoprotein
3D model of the glycosylated spike protein. The glycans are shown in dark magenta, the protein trimer as ribbons. Coordinates for the model can be downloaded from GLYCAM-Web.
Glycosylated spike protein
Species:	SARS-CoV-2
NCBI Protein:	QHR63280.2YP_009724390
UniProtKB Protein:	P0DTC2-1

The SARS-CoV-2 spike glycoprotein is a large type I transmembrane protein with 1273 amino acids. In addition, this protein is highly glycosylated as it contains up to 18 glycans per protomer. SARS-CoV-2 interacts with the host receptor ACE2 which is also a glycoprotein with several known N-linked glycosylation sites.

Model of the glycoprotein

Initial model (3/30/2020)

3D model of the glycosylated spike protein. The glycans are shown in dark magenta, the protein trimer as ribbons. Coordinates for the model can be downloaded from GLYCAM-Web.

An initial model of the glycoprotein based on the PDB structure 6VSB was created by Prof. Dr. Robert Woods' group from the Complex Carbohydrate Research Center of the University of Georgia. For the GlyGen team Dr. Woods stated:

The glycans (biantennary LacNAc N-glycans) are shown in dark magenta, the protein trimer as ribbons. The protein 3D structure is the Swiss-Model homology model, which is based on PDB ID 6VSB. The glycans were built using GLYCAM-Web. There are 18 glycans per protomer, which comprise ~24% of the mass of the spike protein. Coordinates will be made downloadable as soon as the work is published.

The 3D model is available as:

- Animated GIF

- Video

Side specific glycosylation model (4/8/2020)

A second model was release from the Woods' group in early April adding specific reported glycans on each glycosylation side of the protein.

Overlay of snapshots from MD simulation of the S glycoprotein with site-specific glycosylation. The glycans are shown in ball-and-stick representation: M9 (green), M5 (dark yellow), hybrid (orange), complex (pink). The protein surface is colored according to antibody accessibility from black to red (least to most accessible).

The 3D model is available as:

- High resolution SVG

Amino acid sequence

>sp|P0DTC2-1|SPIKE_WCPV Isoform 1 of Spike glycoprotein OS=SARS-CoV-2 OX=2697049 GN=S PE=3 SV=1 CANONICAL=P0DTC2-1
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD
SEPVLKGVKLHYT

External links

PDB link 6VSB

https://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=6VSB

NCBI Taxonmy

• SARS-CoV-2

NCBI Protein

• QHR63280.2