SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL) presented by HLA-A*02:01. Determined by X-ray diffraction at 1.8 Å resolution. Released 15 May 2024.
Explore 8RBV in 3D Show helices and sheets RCSB PDB PDBe
8RBV contains 12 α-helices and 30 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-12 | 10 | 1 |
| α-helix | 20 | 1 | |
| β-strand | 21-28 | 8 | 1 |
| β-strand | 31-37 | 7 | 1 |
| β-strand | 46-47 | 2 | 1 |
| α-helix | 50-52 | 3 | |
| α-helix | 57-84 | 28 | |
| β-strand | 94-103 | 10 | 1 |
| β-strand | 109-118 | 10 | 1 |
| β-strand | 121-126 | 6 | 1 |
| β-strand | 133-135 | 3 | 1 |
| α-helix | 138-149 | 12 | |
| α-helix | 152-158 | 7 | |
| α-helix | 159-163 | 5 | |
| α-helix | 164-174 | 11 | |
| α-helix | 176-179 | 4 | |
| β-strand | 183 | 1 | 2 |
| β-strand | 186-193 | 8 | 3 |
| β-strand | 198-208 | 11 | 3 |
| β-strand | 209 | 1 | 2 |
| β-strand | 214-219 | 6 | 4 |
| β-strand | 222-223 | 2 | 4 |
| β-strand | 228-230 | 3 | 3 |
| α-helix | 231-233 | 3 | |
| β-strand | 234-235 | 2 | 3 |
| β-strand | 241-250 | 10 | 3 |
| α-helix | 254-256 | 3 | |
| β-strand | 257-262 | 6 | 4 |
| β-strand | 270-272 | 3 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3 | 1 | 5 |
| α-helix | 4-5 | 2 | |
| β-strand | 6-11 | 6 | 6 |
| β-strand | 21-30 | 10 | 6 |
| β-strand | 31 | 1 | 5 |
| β-strand | 36-41 | 6 | 7 |
| β-strand | 44-45 | 2 | 7 |
| β-strand | 50-51 | 2 | 6 |
| α-helix | 52-54 | 3 | |
| β-strand | 55-56 | 2 | 6 |
| β-strand | 62-70 | 9 | 6 |
| β-strand | 78-83 | 6 | 7 |
| β-strand | 91-94 | 4 | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| HLA class I antigen | A | protein | 365 | Homo sapiens | Q53Z42 (AlphaFold model) |
| Beta-2-microglobulin | B | protein | 100 | Homo sapiens | P61769 (AlphaFold model) |
| SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant | C | protein | 9 | Severe acute respiratory syndrome coronavirus 2 | P0DTC2 (AlphaFold model) |
>8RBV_1 HLA class I antigen (chains A) MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRF DSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQ RMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQL RAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLT WQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP SSQPTIPIVGIIAGLVLFGAVITGAVVAAVMWRRKSSDRKGGSYSQAASSDSAQGSDVSL TACKV
>8RBV_2 Beta-2-microglobulin (chains B) MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
>8RBV_3 SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (chains C) VLNDILARL
| ID | Name | Formula | Copies |
|---|---|---|---|
| CD | Cadmium ion | Cd | 2 |
Water and common crystallization additives (PEG, EDO, ACT) are not listed.
The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific. Ahn, Y.M., Maddumage, J.C., Grant, E.J. et al. Curr Res Struct Biol (2024) 7:100148-100148. DOI 10.1016/j.crstbi.2024.100148 · PubMed
Other PDB entries of the same protein (UniProt Q53Z42 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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