5YDK: RNF168 UDM1
Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form. Determined by X-ray diffraction at 2.5 Å resolution. Released 7 Mar 2018.
- Method
- X-ray diffraction
- Resolution
- 2.5 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 7,771
- Mol. weight
- 110.39 kDa
- Released
- 7 Mar 2018
Explore 5YDK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5YDK contains 34 α-helices and 56 β-strands across 12 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: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 112-125 | 14 | |
| α-helix | 127-189 | 63 | |
Chain B: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 1 |
| β-strand | 12-16 | 5 | 1 |
| β-strand | 22 | 1 | 2 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 1 |
| β-strand | 48-49 | 2 | 1 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 2 |
| β-strand | 66-71 | 6 | 1 |
| α-helix | 72-73 | 2 | |
Chains C and J: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 11 |
| β-strand | 12-16 | 5 | 11 |
| β-strand | 22 | 1 | 12 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 11 |
| β-strand | 48-49 | 2 | 11 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 12 |
| β-strand | 66-71 | 6 | 11 |
Chain D: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 3 |
| β-strand | 12-16 | 5 | 3 |
| β-strand | 22 | 1 | 4 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 42-45 | 4 | 3 |
| β-strand | 48-49 | 2 | 3 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 4 |
| β-strand | 66-70 | 5 | 3 |
Chain E: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 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 |
Chain F: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 115-117 | 3 | |
| α-helix | 118-190 | 73 | |
Chain G: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 114-125 | 12 | |
| α-helix | 127-190 | 64 | |
Chain H: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 5 |
| β-strand | 12-16 | 5 | 5 |
| β-strand | 22 | 1 | 6 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 5 |
| β-strand | 48-49 | 2 | 5 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 6 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 5 |
| α-helix | 72-73 | 2 | |
3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| E3 ubiquitin-protein ligase RNF168 | A, F, G, L | protein | 87 | Homo sapiens | Q8IYW5 (AlphaFold model) |
| Ubiquitin-40S ribosomal protein S27a | B, E, H, K | protein | 76 | Homo sapiens | P62979 (AlphaFold model) |
| Ubiquitin-40S ribosomal protein S27a | C, D, I, J | protein | 77 | Homo sapiens | P62979 (AlphaFold model) |
Sequence of entity 1 (A, F, G, L), FASTA
>5YDK_1 E3 ubiquitin-protein ligase RNF168 (chains A, F, G, L)
GPGHMPGELRREYEEEISKVAAERRASEEEENKASEEYIQRLLAEEEEEEKRQAEKRRRA
MEEQLKSDEELARKLSIDINNFCEGSI
Sequence of entity 2 (B, E, H, K), FASTA
>5YDK_2 Ubiquitin-40S ribosomal protein S27a (chains B, E, H, K)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQRESTLHLVLRLRGG
Sequence of entity 3 (C, D, I, J), FASTA
>5YDK_3 Ubiquitin-40S ribosomal protein S27a (chains C, D, I, J)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGD
Primary citation
Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168. Takahashi, T.S., Hirade, Y., Toma, A. et al. Nat Commun (2018) 9:170-170. DOI 10.1038/s41467-017-02345-y · PubMed
Other PDB entries of the same protein (UniProt Q8IYW5 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5XIS 1.78 Å, Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I
- 5XIU 1.8 Å, Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin
- 8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
- 3L11 2.12 Å, Crystal Structure of the Ring Domain of RNF168
- 5XIT 2.25 Å, Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II
- 8UQ9 2.3 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker
- 8UQ8 2.34 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker
- 8UQB 2.48 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
- 4GB0 2.6 Å, Crystal Structure of the RING domain of RNF168
- 8UQC 2.61 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
- 8SMX 3.2 Å, Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and…
- 8SMY 3.2 Å, Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and…
Browse structure collections
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