Crystal structure of Proinsulin C-peptide bound to HLA-DQ8. Determined by X-ray diffraction at 2.6 Å resolution. Released 7 Aug 2024.
Explore 8VDD in 3D Show helices and sheets RCSB PDB PDBe
8VDD contains 15 α-helices and 30 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 | 20-27 | 8 | 1 |
| β-strand | 30-36 | 7 | 1 |
| β-strand | 41-44 | 4 | 1 |
| α-helix | 47-52 | 6 | |
| β-strand | 54 | 1 | 2 |
| α-helix | 57-77 | 21 | |
| α-helix | 82-86 | 5 | |
| β-strand | 89-94 | 6 | 3 |
| β-strand | 104-113 | 10 | 3 |
| β-strand | 119-123 | 5 | 4 |
| β-strand | 128-129 | 2 | 4 |
| β-strand | 133-135 | 3 | 3 |
| α-helix | 136-138 | 3 | |
| β-strand | 139-140 | 2 | 3 |
| β-strand | 146-154 | 9 | 3 |
| β-strand | 162-167 | 6 | 4 |
| β-strand | 175-179 | 5 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 8-18 | 11 | 1 |
| β-strand | 23-32 | 10 | 1 |
| β-strand | 35-41 | 7 | 1 |
| β-strand | 47-49 | 3 | 1 |
| α-helix | 55-63 | 9 | |
| α-helix | 65-72 | 8 | |
| α-helix | 74 | 1 | |
| α-helix | 75-80 | 6 | |
| α-helix | 81-87 | 7 | |
| α-helix | 90-92 | 3 | |
| β-strand | 95 | 1 | 5 |
| α-helix | 96-97 | 2 | |
| β-strand | 98-102 | 5 | 6 |
| β-strand | 115-122 | 8 | 6 |
| β-strand | 123 | 1 | 5 |
| β-strand | 128-133 | 6 | 7 |
| β-strand | 136-138 | 3 | 7 |
| β-strand | 142-144 | 3 | 6 |
| α-helix | 145-147 | 3 | |
| β-strand | 148-149 | 2 | 6 |
| β-strand | 155-161 | 7 | 6 |
| β-strand | 171-176 | 6 | 7 |
| β-strand | 184-188 | 5 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | -1 | 1 | |
| β-strand | 0 | 1 | 2 |
| α-helix | 1 | 1 | |
| α-helix | 4-9 | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| MHC class II HLA-DQ-alpha chain | A | protein | 185 | Homo sapiens | Q30069 (AlphaFold model) |
| MHC class II HLA-DQ-beta-1 | B | protein | 192 | Homo sapiens | O19707 (AlphaFold model) |
| Proinsulin C-peptide (InsC8-22) | C | protein | 15 | Homo sapiens | P01308 (AlphaFold model) |
>8VDD_1 MHC class II HLA-DQ-alpha chain (chains A) EDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQ FALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVV NITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKH WEPES
>8VDD_2 MHC class II HLA-DQ-beta-1 (chains B) RDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEY WNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVT DFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSL QNPIIVEWRAQS
>8VDD_3 Proinsulin C-peptide (InsC8-22) (chains C) GQVELGGGPGAESCQ
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
Water and common crystallization additives (GOL) are not listed.
A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8. Tran, M.T., Lim, J.J., Loh, T.J. et al. J Biol Chem (2024) 300:107612-107612. DOI 10.1016/j.jbc.2024.107612 · PubMed
Other PDB entries of the same protein (UniProt Q30069 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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