5FER: Complex of TRIM25 RING with UbcH5-Ub
Complex of TRIM25 RING with UbcH5-Ub. Determined by X-ray diffraction at 2.34 Å resolution. Released 18 May 2016.
- Method
- X-ray diffraction
- Resolution
- 2.34 Å
- Organisms
- Homo sapiens, Bos taurus
- Chains
- 6
- Atoms
- 4,832
- Mol. weight
- 69.83 kDa
- Ligands
- ZN
- Released
- 18 May 2016
Explore 5FER in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5FER contains 27 α-helices and 48 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: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| β-strand | 12 | 1 | 1 |
| β-strand | 19 | 1 | 1 |
| β-strand | 23-25 | 3 | 2 |
| β-strand | 31-33 | 3 | 2 |
| α-helix | 34-43 | 10 | |
| β-strand | 48-49 | 2 | 3 |
| β-strand | 56-57 | 2 | 3 |
| α-helix | 60-61 | 2 | |
| β-strand | 65 | 1 | 2 |
| α-helix | 67-78 | 12 | |
Chain B: 6 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-15 | 14 | |
| β-strand | 21-24 | 4 | 4 |
| β-strand | 32-38 | 7 | 4 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 4 |
| β-strand | 66-69 | 4 | 4 |
| β-strand | 75 | 1 | 5 |
| β-strand | 78 | 1 | 5 |
| β-strand | 83 | 1 | 4 |
| β-strand | 84 | 1 | 5 |
| β-strand | 86 | 1 | 6 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-110 | 12 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-144 | 14 | |
Chain C: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 7 |
| β-strand | 12-16 | 5 | 7 |
| β-strand | 22 | 1 | 8 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 7 |
| β-strand | 48-49 | 2 | 7 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 8 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 7 |
| β-strand | 75 | 1 | 6 |
Chain D: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| β-strand | 12 | 1 | 9 |
| β-strand | 19 | 1 | 9 |
| β-strand | 23-25 | 3 | 10 |
| β-strand | 31-33 | 3 | 10 |
| α-helix | 34-42 | 9 | |
| β-strand | 48-49 | 2 | 11 |
| β-strand | 56-57 | 2 | 11 |
| α-helix | 60-61 | 2 | |
| β-strand | 65 | 1 | 10 |
| α-helix | 67-81 | 15 | |
Chain E: 7 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-15 | 14 | |
| β-strand | 21-25 | 5 | 12 |
| β-strand | 32-38 | 7 | 12 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 12 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 12 |
| β-strand | 75 | 1 | 13 |
| β-strand | 78 | 1 | 13 |
| β-strand | 83 | 1 | 12 |
| β-strand | 84 | 1 | 13 |
| β-strand | 86 | 1 | 14 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-110 | 12 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-144 | 14 | |
Chain F: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 15 |
| β-strand | 12-16 | 5 | 15 |
| β-strand | 22 | 1 | 16 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 15 |
| β-strand | 48-49 | 2 | 15 |
| β-strand | 55 | 1 | 16 |
| β-strand | 66-71 | 6 | 15 |
| β-strand | 75 | 1 | 14 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| E3 ubiquitin/ISG15 ligase TRIM25 | A, D | protein | 85 | Homo sapiens | Q14258 (AlphaFold model) |
| Ubiquitin-conjugating enzyme E2 D1 | B, E | protein | 150 | Homo sapiens | P51668 (AlphaFold model) |
| Ubiquitin-40S ribosomal protein S27a | C, F | protein | 76 | Bos taurus | P62992 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>5FER_1 E3 ubiquitin/ISG15 ligase TRIM25 (chains A, D)
GPGMAELCPLAEELSCSICLEPFKEPVTTPCGHNFCGSCLNETWAVQGSPYLCPQCRAVY
QARPQLHKNTVLCNVVEQFLQADLA
Sequence of entity 2 (B, E), FASTA
>5FER_2 Ubiquitin-conjugating enzyme E2 D1 (chains B, E)
GPGMALKRIQKELSDLQRDPPAHCRAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFP
TDYPFKPPKIAFTTKIYHPNINSNGSIKLDILRSQWSPALTVSKVLLSICSLLCDPNPDD
PLVPDIAQIYKSDKEKYNRHAREWTQKYAM
Sequence of entity 3 (C, F), FASTA
>5FER_3 Ubiquitin-40S ribosomal protein S27a (chains C, F)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity. Koliopoulos, M.G., Esposito, D., Christodoulou, E. et al. EMBO J (2016) 35:1204-1218. DOI 10.15252/embj.201593741 · PubMed
Other PDB entries of the same protein (UniProt Q14258 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9I0T 1.8 Å, Crystal structure of TRIM25 PRYSPRY covalently bound to…
- 6FLM 2.01 Å, Crystal structure of the human TRIM25 PRYSPRY domain
- 5EYA 2.4 Å, TRIM25 RING domain in complex with Ubc13-Ub conjugate
- 4LTB 2.59 Å, Coiled-coil domain of TRIM25
- 9IUN 2.7 Å, Crystal structure of Trim25 Pspry
- 4CFG 2.8 Å, Structure of the TRIM25 coiled-coil
- 5NT1 2.82 Å, Complex of influenza A NS1 effector domain with TRIM25 coiled coil
- 6FLN 3.6 Å, Crystal structure of the human TRIM25 coiled-coil and PRYSPRY domains
- 5NT2 4.26 Å, Complex of influenza A NS1 with TRIM25 coiled coil domain
Browse structure collections
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