Ternary trans-complex of phospho-parkin with cis ACT and pUb. Determined by X-ray diffraction at 2.6 Å resolution. Released 11 Sept 2024.
Explore 8IKT in 3D Show helices and sheets RCSB PDB PDBe
8IKT contains 12 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 | 146-150 | 5 | 1 |
| β-strand | 156-159 | 4 | 1 |
| β-strand | 160-166 | 7 | 2 |
| β-strand | 174-176 | 3 | 3 |
| α-helix | 183-187 | 5 | |
| β-strand | 193 | 1 | 4 |
| β-strand | 194-196 | 3 | 3 |
| β-strand | 205 | 1 | 4 |
| β-strand | 206-212 | 7 | 2 |
| β-strand | 224-230 | 7 | 1 |
| α-helix | 236-238 | 3 | |
| β-strand | 248-250 | 3 | 1 |
| β-strand | 258-260 | 3 | 1 |
| α-helix | 261-273 | 13 | |
| α-helix | 277 | 1 | |
| β-strand | 278-280 | 3 | 5 |
| β-strand | 284-286 | 3 | 5 |
| α-helix | 301-307 | 7 | |
| α-helix | 309-326 | 18 | |
| β-strand | 330-331 | 2 | 6 |
| β-strand | 340-342 | 3 | 6 |
| β-strand | 349-351 | 3 | 7 |
| β-strand | 363-365 | 3 | 7 |
| β-strand | 371 | 1 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-7 | 6 | 6 |
| β-strand | 12-16 | 5 | 6 |
| β-strand | 22 | 1 | 8 |
| α-helix | 23-34 | 12 | |
| β-strand | 41-45 | 5 | 6 |
| β-strand | 48-49 | 2 | 6 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 8 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-72 | 7 | 6 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-7 | 6 | 9 |
| β-strand | 13-16 | 4 | 9 |
| β-strand | 22 | 1 | 10 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 9 |
| β-strand | 48-50 | 3 | 9 |
| α-helix | 51 | 1 | |
| β-strand | 55 | 1 | 10 |
| β-strand | 66-71 | 6 | 9 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| E3 ubiquitin-protein ligase parkin | A | protein | 312 | Homo sapiens | O60260 (AlphaFold model) |
| Ubiquitin | B | protein | 75 | Homo sapiens | P62987 (AlphaFold model) |
| E3 ubiquitin-protein ligase parkin | C | protein | 76 | Homo sapiens | O60260 (AlphaFold model) |
>8IKT_1 E3 ubiquitin-protein ligase parkin (chains A) SGQEMNATGGDDPRNAAGGCEREPQSLTRVDLSSSVLPGDSVGLAVILHTDSRKDSPPAG SPAGRSIYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGE CQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNS RHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRY QQYGAEECVLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGLGCGFAFCRECKEAYHEG ECSAVFENLYFQ
>8IKT_2 Ubiquitin (chains B) MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRG
>8IKT_3 E3 ubiquitin-protein ligase parkin (chains C) MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCD LDQQSIVHIVQRPWRK
Water and common crystallization additives (MPD, GOL) are not listed.
Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans. Lenka, D.R., Dahe, S.V., Antico, O. et al. Elife (2024) 13. DOI 10.7554/eLife.96699 · PubMed
Other PDB entries of the same protein (UniProt O60260 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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