HLA-DRB1 in complex with citrullinated Vimentin peptide. Determined by X-ray diffraction at 2.3 Å resolution. Released 17 Jan 2018.
Explore 6BIR in 3D Show helices and sheets RCSB PDB PDBe
6BIR 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 | 56-76 | 21 | |
| α-helix | 80-84 | 5 | |
| β-strand | 85 | 1 | 3 |
| 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 | |
| β-strand | 95 | 1 | 6 |
| α-helix | 96-97 | 2 | |
| β-strand | 98-104 | 7 | 7 |
| β-strand | 114-122 | 9 | 7 |
| β-strand | 123 | 1 | 6 |
| β-strand | 128-133 | 6 | 8 |
| β-strand | 136-137 | 2 | 8 |
| β-strand | 142-144 | 3 | 7 |
| β-strand | 148-149 | 2 | 7 |
| β-strand | 155-162 | 8 | 7 |
| α-helix | 165-166 | 2 | |
| β-strand | 170-176 | 7 | 8 |
| β-strand | 184-189 | 6 | 8 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2 | 1 | 2 |
| α-helix | 3-5 | 3 | |
| α-helix | 7-10 | 4 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| HLA class II histocompatibility antigen, DR alpha chain | A | protein | 189 | Homo sapiens | P01903 (AlphaFold model) |
| MHC class II antigen | B | protein | 200 | Homo sapiens | P01911 (AlphaFold model) |
| Vimentin 424Cit419-431 | C | protein | 13 | Homo sapiens | P08670 (AlphaFold model) |
>6BIR_1 HLA class II histocompatibility antigen, DR alpha chain (chains A) IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF DTSGDDDDK
>6BIR_2 MHC class II antigen (chains B) GSGDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPSA EYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCS VNGFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHP SLTSPLTVEWRATGGDDDDK
>6BIR_3 Vimentin 424Cit419-431 (chains C) SSLNLRETNLDSL
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
The interplay between citrullination and HLA-DRB1 polymorphism in shaping peptide binding hierarchies in rheumatoid arthritis. Ting, Y.T., Petersen, J., Ramarathinam, S.H. et al. J Biol Chem (2018) 293:3236-3251. DOI 10.1074/jbc.RA117.001013 · 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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