Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340 (arginine 327 to citrulline). Determined by X-ray diffraction at 1.35 Å resolution. Released 13 Jun 2018.
Explore 5NIG in 3D Show helices and sheets RCSB PDB PDBe
5NIG 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 | 46-50 | 5 | |
| β-strand | 53 | 1 | 2 |
| α-helix | 57-76 | 20 | |
| 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 |
| 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 |
| α-helix | 190-193 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 327 | 1 | 2 |
| α-helix | 328-337 | 10 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| HLA class II histocompatibility antigen, DR alpha chain | A | protein | 189 | Homo sapiens | P01903 (AlphaFold model) |
| HLA class II histocompatibility antigen, DRB1-4 beta chain | B | protein | 198 | Homo sapiens | P01911 (AlphaFold model) |
| Alpha-enolase | C | protein | 15 | Homo sapiens | P06733 (AlphaFold model) |
>5NIG_1 HLA class II histocompatibility antigen, DR alpha chain (chains A) IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF DSSADLVPR
>5NIG_2 HLA class II histocompatibility antigen, DRB1-4 beta chain (chains B) GDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEY WNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVN GFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSL TSPLTVEWRASSADLVPR
>5NIG_3 Alpha-enolase (chains C) KRIAKAVNEKSCNCL
| ID | Name | Formula | Copies |
|---|---|---|---|
| URE | Urea | C H4 N2 O | 1 |
Water and common crystallization additives (MPD, PGE) are not listed.
Memory T cells specific to citrullinated alpha-enolase are enriched in the rheumatic joint. Pieper, J., Dubnovitsky, A., Gerstner, C. et al. J Autoimmun (2018) 92:47-56. DOI 10.1016/j.jaut.2018.04.004 · 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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