4UF6: UCH-L5
UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G. Determined by X-ray diffraction at 3.69 Å resolution. Released 4 Mar 2015.
- Method
- X-ray diffraction
- Resolution
- 3.69 Å
- Organism
- HOMO SAPIENS
- Chains
- 12
- Atoms
- 13,486
- Mol. weight
- 215.07 kDa
- Released
- 4 Mar 2015
Explore 4UF6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4UF6 contains 98 α-helices and 80 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: 18 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| β-strand | 12 | 1 | 1 |
| α-helix | 15-24 | 10 | |
| β-strand | 28 | 1 | 2 |
| β-strand | 30-34 | 5 | 3 |
| α-helix | 41-44 | 4 | |
| α-helix | 47 | 1 | |
| β-strand | 49-57 | 9 | 3 |
| α-helix | 62-64 | 3 | |
| β-strand | 67-68 | 2 | 3 |
| α-helix | 69 | 1 | |
| α-helix | 73-76 | 4 | |
| α-helix | 88-97 | 10 | |
| β-strand | 106 | 1 | 2 |
| α-helix | 109-118 | 10 | |
| α-helix | 123-132 | 10 | |
| α-helix | 134-141 | 8 | |
| α-helix | 144-147 | 4 | |
| β-strand | 163-171 | 9 | 3 |
| β-strand | 174-178 | 5 | 3 |
| α-helix | 185 | 1 | |
| β-strand | 186-190 | 5 | 3 |
| β-strand | 192 | 1 | 4 |
| β-strand | 195 | 1 | 4 |
| α-helix | 197-209 | 13 | |
| β-strand | 218-225 | 8 | 3 |
| α-helix | 227-244 | 18 | |
| α-helix | 258-288 | 31 | |
| α-helix | 292-304 | 13 | |
| α-helix | 308-317 | 10 | |
Chains B, E, H and K: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 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 |
| β-strand | 55 | 1 | 6 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 5 |
| β-strand | 74 | 1 | 1 |
Chains C and F: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-60 | 14 | |
| α-helix | 65-72 | 8 | |
| α-helix | 81-92 | 12 | |
Chains D and J: 18 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| β-strand | 12 | 1 | 7 |
| α-helix | 15-24 | 10 | |
| β-strand | 28 | 1 | 8 |
| β-strand | 30-34 | 5 | 9 |
| α-helix | 41-44 | 4 | |
| α-helix | 47 | 1 | |
| β-strand | 49-57 | 9 | 9 |
| α-helix | 62-64 | 3 | |
| β-strand | 67-68 | 2 | 9 |
| α-helix | 69 | 1 | |
| α-helix | 73-76 | 4 | |
| α-helix | 88-97 | 10 | |
| β-strand | 106 | 1 | 8 |
| α-helix | 109-118 | 10 | |
| α-helix | 123-132 | 10 | |
| α-helix | 134-141 | 8 | |
| α-helix | 144-146 | 3 | |
| β-strand | 163-171 | 9 | 9 |
| β-strand | 174-178 | 5 | 9 |
| α-helix | 185 | 1 | |
| β-strand | 186-190 | 5 | 9 |
| β-strand | 192 | 1 | 10 |
| β-strand | 195 | 1 | 10 |
| α-helix | 197-209 | 13 | |
| β-strand | 218-225 | 8 | 9 |
| α-helix | 227-244 | 18 | |
| α-helix | 258-288 | 31 | |
| α-helix | 292-304 | 13 | |
| α-helix | 308-317 | 10 | |
Chain G: 18 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| β-strand | 12 | 1 | 13 |
| α-helix | 15-24 | 10 | |
| β-strand | 28 | 1 | 14 |
| β-strand | 30-34 | 5 | 15 |
| α-helix | 41-44 | 4 | |
| α-helix | 47 | 1 | |
| β-strand | 49-57 | 9 | 15 |
| α-helix | 62-64 | 3 | |
| β-strand | 67-68 | 2 | 15 |
| α-helix | 69 | 1 | |
| α-helix | 73-76 | 4 | |
| α-helix | 88-97 | 10 | |
| β-strand | 106 | 1 | 14 |
| α-helix | 108-117 | 10 | |
| α-helix | 118-120 | 3 | |
| α-helix | 123-132 | 10 | |
| α-helix | 134-141 | 8 | |
| β-strand | 163-171 | 9 | 15 |
| β-strand | 174-178 | 5 | 15 |
| α-helix | 185 | 1 | |
| β-strand | 186-190 | 5 | 15 |
| β-strand | 192 | 1 | 16 |
| β-strand | 195 | 1 | 16 |
| α-helix | 197-209 | 13 | |
| β-strand | 218-225 | 8 | 15 |
| α-helix | 227-242 | 16 | |
| α-helix | 258-288 | 31 | |
| α-helix | 292-304 | 13 | |
| α-helix | 308-317 | 10 | |
Chains I and L: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-60 | 14 | |
| α-helix | 65-72 | 8 | |
| α-helix | 75-77 | 3 | |
| α-helix | 81-91 | 11 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin carboxyl-terminal hydrolase isozyme L5 | A, D, G, J | protein | 331 | HOMO SAPIENS | Q9Y5K5 (AlphaFold model) |
| Polyubiquitin-B | B, E, H, K | protein | 76 | HOMO SAPIENS | P0CG47 (AlphaFold model) |
| Nuclear factor related to kappa-B-binding protein | C, F, I, L | protein | 65 | HOMO SAPIENS | Q6P4R8 (AlphaFold model) |
Sequence of entity 1 (A, D, G, J), FASTA
>4UF6_1 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 (chains A, D, G, J)
GPGMTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFK
WQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEF
SQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYE
LDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAE
LQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIME
LLKTLAEHQQLIPLVEKAKEKQNAKKAQETK
Sequence of entity 2 (B, E, H, K), FASTA
>4UF6_2 POLYUBIQUITIN-B (chains B, E, H, K)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGX
Sequence of entity 3 (C, F, I, L), FASTA
>4UF6_3 NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN (chains C, F, I, L)
GPGEDLLEDPEIFFDVVSLSTWQEVLSDSQREHLQQFLPQFPEDSAEQQNELILALFSGE
NFRFG
Primary citation
Mechanism of Uch-L5 Activation and Inhibition by Deubad Domains in Rpn13 and Ino80G. Sahtoe, D.D., Van Dijk, W.J., El Oualid, F. et al. Mol Cell (2015) 57:887. DOI 10.1016/J.MOLCEL.2014.12.039 · PubMed
Other PDB entries of the same protein (UniProt Q9Y5K5 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3RII 2.0 Å, Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human…
- 3A7S 2.2 Å, Catalytic domain of UCH37
- 3TB3 2.3 Å, Crystal structure of the UCH domain of UCH-L5 with 6 residues deleted
- 4UEL 2.3 Å, UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain
- 3RIS 2.4 Å, Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human…
- 9E7K 2.41 Å, Crystal structure of the UCH37 RPN13 DEUBAD complex bound to an inhibitory nanobody in…
- 4UEM 2.82 Å, UCH-L5 in complex with the RPN13 DEUBAD domain
- 3IHR 2.95 Å, Crystal Structure of Uch37
- 4WLP 3.1 Å, Crystal structure of UCH37-NFRKB Inhibited Deubiquitylating Complex
- 4UF5 3.7 Å, Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G
Browse structure collections
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