FP-HR1-CH-CD-SH-HR2-TM
The fusion peptide (FP) is a short hydrophobic region located at the N-terminus of the S2 subunit of the spike protein. Its primary role is to facilitate the fusion of the viral membrane with the host cell membrane. When the virus is ready to enter the host cell, the fusion peptide is exposed and inserts itself into the host membrane, initiating the fusion process.
Heptad Repeat 1 (HR1) is a region within the S2 subunit that contains repeating sequences of seven amino acids. HR1 is critical for the formation of a six-helix bundle structure during the fusion process. It interacts with HR2 to bring the viral and host membranes close together, allowing fusion to occur.
The central helix (CH) is a structural element that connects the heptad repeats (HR1 and HR2) and plays a role in the stability of the six-helix bundle formed during fusion.
The Connector Domain (CD) plays a crucial role in maintaining structural integrity and functional connectivity between the various domains of the spike protein. It helps in the proper assembly and interaction between HR1 and HR2, which is critical for the fusion process.
Heptad Repeat 2 (HR2) is another heptad repeat region located within the S2 subunit. HR2 interacts with HR1 to form the six-helix bundle structure, which is crucial for the fusion of the viral and host membranes.
The transmembrane domain (TM) is a segment of the spike protein that spans the viral membrane and anchors the protein to the viral envelope. It plays a role in stabilizing the spike protein and is involved in the final steps of the fusion process.
| № | Extended PDB ID | PDB ID | Method | Resolution | Chain | Start | End | Macromolecules | Ligand 1 | Ligand 2 |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | pdb_00008dya | 8DYA | EM | 3.67 A | A/B/C | 686 | 1208 | Spike glycoprotein | - | - |
| 2 | pdb_00008vq9 | 8VQ9 | EM | 2.70 A | A/B/C | 686 | 1208 | Spike protein S2 | - | - |
| 3 | pdb_00008vqa | 8VQA | EM | 3.50 A | A/B/C | 686 | 1208 | Spike protein S2 | - | - |
| 4 | pdb_00008vqb | 8VQB | EM | 3.00 A | A/B/C | 686 | 1208 | Spike protein S2 | - | - |
| 5 | pdb_00008vao | 8VAO | EM | 2.80 A | A/B/C | 697 | 1208 | Spike protein S2 | - | - |
| 6 | pdb_00008vcr | 8VCR | EM | 3.00 A | A/B/C | 697 | 1208 | Spike protein S2 | 54043-5 Fab Heavy Chain | 54043-5 Fab Light Chain |
| 7 | pdb_00008u1g | 8U1G | X-ray | 3.20 A | A/B | 697 | 1141 | Spike glycoprotein | - | - |
| 8 | pdb_00007e9t | 7E9T | EM | 10.90 A | A/B/C | 703 | 1234 | Spike glycoprotein | - | - |
| 9 | pdb_00008fdw | 8FDW | EM | 2.90 A | A/B/C | 686 | 1273 | Spike glycoprotein | - | - |