5B83: Optineurin UBAN
Crystal structure of Optineurin UBAN in complex with linear ubiquitin. Determined by X-ray diffraction at 2.69 Å resolution. Released 7 Sept 2016.
- Method
- X-ray diffraction
- Resolution
- 2.69 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 6,702
- Mol. weight
- 114.97 kDa
- Released
- 7 Sept 2016
Explore 5B83 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5B83 contains 34 α-helices and 56 β-strands across 6 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.
Chain A: 13 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 1 |
| β-strand | 12-15 | 4 | 1 |
| β-strand | 22 | 1 | 2 |
| α-helix | 23-31 | 9 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 1 |
| β-strand | 48-50 | 3 | 1 |
| β-strand | 55 | 1 | 2 |
| α-helix | 56-58 | 3 | |
| α-helix | 65 | 1 | |
| β-strand | 66-71 | 6 | 1 |
| β-strand | 77-82 | 6 | 3 |
| β-strand | 88-93 | 6 | 3 |
| β-strand | 98 | 1 | 4 |
| α-helix | 99-110 | 12 | |
| α-helix | 114-116 | 3 | |
| β-strand | 117-121 | 5 | 3 |
| β-strand | 124-125 | 2 | 3 |
| β-strand | 131 | 1 | 4 |
| β-strand | 142-147 | 6 | 3 |
| β-strand | 153-158 | 6 | 5 |
| β-strand | 164-169 | 6 | 5 |
| β-strand | 174 | 1 | 6 |
| α-helix | 175-186 | 12 | |
| α-helix | 190-192 | 3 | |
| β-strand | 193-197 | 5 | 5 |
| β-strand | 200-201 | 2 | 5 |
| α-helix | 202-203 | 2 | |
| β-strand | 207 | 1 | 6 |
| β-strand | 218-223 | 6 | 5 |
| β-strand | 230-234 | 5 | 7 |
| β-strand | 240-244 | 5 | 7 |
| β-strand | 250 | 1 | 8 |
| α-helix | 251-262 | 12 | |
| α-helix | 266-268 | 3 | |
| β-strand | 269-273 | 5 | 7 |
| β-strand | 276-277 | 2 | 7 |
| α-helix | 278-279 | 2 | |
| β-strand | 283 | 1 | 8 |
| α-helix | 285-287 | 3 | |
| β-strand | 294-299 | 6 | 7 |
Chain B: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 447-497 | 51 | |
Chain C: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 448-457 | 10 | |
| α-helix | 460-502 | 43 | |
Chain D: 16 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 9 |
| β-strand | 12-16 | 5 | 9 |
| β-strand | 22 | 1 | 10 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-44 | 4 | 9 |
| β-strand | 49 | 1 | 9 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 10 |
| β-strand | 66-71 | 6 | 9 |
| β-strand | 77-83 | 7 | 11 |
| β-strand | 88-93 | 6 | 11 |
| β-strand | 98 | 1 | 12 |
| α-helix | 99-110 | 12 | |
| α-helix | 114-116 | 3 | |
| β-strand | 117-121 | 5 | 11 |
| β-strand | 124-125 | 2 | 11 |
| α-helix | 126-127 | 2 | |
| β-strand | 131 | 1 | 12 |
| α-helix | 137-138 | 2 | |
| α-helix | 141 | 1 | |
| β-strand | 142-147 | 6 | 11 |
| α-helix | 149-151 | 3 | |
| β-strand | 153-159 | 7 | 13 |
| β-strand | 164-169 | 6 | 13 |
| β-strand | 174 | 1 | 14 |
| α-helix | 175-186 | 12 | |
| α-helix | 190-192 | 3 | |
| β-strand | 193-197 | 5 | 13 |
| β-strand | 200-201 | 2 | 13 |
| α-helix | 202-203 | 2 | |
| β-strand | 207 | 1 | 14 |
| α-helix | 209-211 | 3 | |
| β-strand | 218-223 | 6 | 13 |
| β-strand | 229-235 | 7 | 15 |
| β-strand | 240-245 | 6 | 15 |
| β-strand | 250 | 1 | 16 |
| α-helix | 251-262 | 12 | |
| α-helix | 266-268 | 3 | |
| β-strand | 270-273 | 4 | 15 |
| β-strand | 276-277 | 2 | 15 |
| α-helix | 278-279 | 2 | |
| β-strand | 283 | 1 | 16 |
| β-strand | 294-298 | 5 | 15 |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 458-499 | 42 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 449-499 | 51 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| tetra ubiquitin | A, D | protein | 304 | Homo sapiens | P0CG48 (AlphaFold model) |
| Optineurin | B, C, E, F | protein | 102 | Homo sapiens | Q96CV9 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>5B83_1 tetra ubiquitin (chains A, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI
FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKA
KIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKT
ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR
LRGG
Sequence of entity 2 (B, C, E, F), FASTA
>5B83_2 Optineurin (chains B, C, E, F)
GPLGSHMEKVDRAVLKELSEKLELAEKALASKQLQMDEMKQTIAKQEEDLETMTILRAQM
EVYCSDFHAERAAREKIHEEKEQLALQLAVLLKENDAFEDGG
Primary citation
Linear ubiquitination is involved in the pathogenesis of optineurin-associated amyotrophic lateral sclerosis. Nakazawa, S., Oikawa, D., Ishii, R. et al. Nat Commun (2016) 7:12547-12547. DOI 10.1038/ncomms12547 · PubMed
Other PDB entries of the same protein (UniProt P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
- 1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
- 5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
- 2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
- 4HK2 1.4 Å, U7Ub25.2540
- 9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
- 1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
- 4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
- 7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
- 5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
- 9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
- 9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant
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