Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S486-505. Determined by X-ray diffraction at 1.64 Å resolution. Released 26 Jul 2023.
Explore 8CMH in 3D Show helices and sheets RCSB PDB PDBe
8CMH contains 13 α-helices and 32 β-strands across 3 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 | 5-15 | 11 | 1 |
| β-strand | 19-26 | 8 | 1 |
| β-strand | 29-35 | 7 | 1 |
| β-strand | 40-43 | 4 | 1 |
| α-helix | 48-51 | 4 | |
| β-strand | 53 | 1 | 2 |
| α-helix | 56-76 | 21 | |
| α-helix | 80-84 | 5 | |
| β-strand | 85 | 1 | 3 |
| α-helix | 86-87 | 2 | |
| β-strand | 88-93 | 6 | 4 |
| β-strand | 103-112 | 10 | 4 |
| β-strand | 113 | 1 | 3 |
| β-strand | 118-123 | 6 | 5 |
| β-strand | 126-127 | 2 | 5 |
| β-strand | 133-134 | 2 | 4 |
| α-helix | 137 | 1 | |
| β-strand | 138-139 | 2 | 4 |
| β-strand | 145-153 | 9 | 4 |
| β-strand | 160-166 | 7 | 5 |
| β-strand | 174-179 | 6 | 5 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 7-18 | 12 | 1 |
| β-strand | 23-32 | 10 | 1 |
| β-strand | 35-41 | 7 | 1 |
| β-strand | 47-49 | 3 | 1 |
| α-helix | 52-54 | 3 | |
| α-helix | 55-62 | 8 | |
| α-helix | 65-74 | 10 | |
| α-helix | 75-80 | 6 | |
| α-helix | 81-86 | 6 | |
| α-helix | 87-89 | 3 | |
| β-strand | 95 | 1 | 6 |
| α-helix | 96-97 | 2 | |
| β-strand | 98-103 | 6 | 7 |
| β-strand | 113-122 | 10 | 7 |
| β-strand | 123 | 1 | 6 |
| β-strand | 128-133 | 6 | 8 |
| β-strand | 136-138 | 3 | 8 |
| β-strand | 142-144 | 3 | 7 |
| β-strand | 148-149 | 2 | 7 |
| β-strand | 155-163 | 9 | 7 |
| β-strand | 170-176 | 7 | 8 |
| β-strand | 184-189 | 6 | 8 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3 | 1 | 2 |
| α-helix | 4-9 | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| HLA class II histocompatibility antigen, DR alpha chain | A | protein | 183 | Homo sapiens | P01903 (AlphaFold model) |
| Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101) | B | protein | 194 | Homo sapiens | D7RIG0 (AlphaFold model) |
| Spike protein S2' | C | protein | 20 | Severe acute respiratory syndrome coronavirus 2 | P0DTC2 (AlphaFold model) |
>8CMH_1 HLA class II histocompatibility antigen, DR alpha chain (chains A) MIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGA LANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNV TWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWE FDA
>8CMH_2 Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101) (chains B) MGSMGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRP DAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLV CSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVE HPSVTSPLTVEWRA
>8CMH_3 Spike protein S2' (chains C) FNCYFPLRSYSFRPTYGVGH
| ID | Name | Formula | Copies |
|---|---|---|---|
| DHL | 2-amino-ethanethiol | C2 H7 N S | 1 |
Water and common crystallization additives (EDO, SO4) are not listed.
Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity. Chen, Y., Mason, G.H., Scourfield, D.O. et al. Cell Rep (2023) 42:112827-112827. DOI 10.1016/j.celrep.2023.112827 · PubMed
Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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