5EYA: TRIM25 RING domain
TRIM25 RING domain in complex with Ubc13-Ub conjugate. Determined by X-ray diffraction at 2.4 Å resolution. Released 17 Aug 2016.
- Method
- X-ray diffraction
- Resolution
- 2.4 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 5,018
- Mol. weight
- 70.79 kDa
- Ligands
- ZN
- Released
- 17 Aug 2016
Explore 5EYA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5EYA 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.
Chains A and B: 8 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-17 | 12 | |
| α-helix | 19-20 | 2 | |
| β-strand | 23-28 | 6 | 1 |
| β-strand | 31-40 | 10 | 1 |
| α-helix | 41-42 | 2 | |
| β-strand | 51-57 | 7 | 1 |
| α-helix | 66-67 | 2 | |
| β-strand | 68-71 | 4 | 1 |
| β-strand | 77 | 1 | 2 |
| β-strand | 80 | 1 | 2 |
| β-strand | 85 | 1 | 1 |
| β-strand | 86 | 1 | 2 |
| β-strand | 88 | 1 | 3 |
| α-helix | 89-91 | 3 | |
| α-helix | 101-113 | 13 | |
| α-helix | 123-131 | 9 | |
| α-helix | 133-147 | 15 | |
Chain C: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 13 |
| α-helix | 11 | 1 | |
| β-strand | 12-16 | 5 | 13 |
| β-strand | 22 | 1 | 14 |
| α-helix | 23-34 | 12 | |
| β-strand | 41-45 | 5 | 13 |
| β-strand | 48-49 | 2 | 13 |
| β-strand | 55 | 1 | 14 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 13 |
| β-strand | 75 | 1 | 12 |
Chain D: 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 | 3 |
Chain F: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| β-strand | 12 | 1 | 4 |
| β-strand | 19 | 1 | 4 |
| β-strand | 23-25 | 3 | 5 |
| β-strand | 31-33 | 3 | 5 |
| α-helix | 34-43 | 10 | |
| β-strand | 48-49 | 2 | 6 |
| β-strand | 56-57 | 2 | 6 |
| β-strand | 65 | 1 | 5 |
| α-helix | 67-80 | 14 | |
Chain G: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-7 | 6 | |
| β-strand | 12 | 1 | 7 |
| β-strand | 19 | 1 | 7 |
| β-strand | 23-25 | 3 | 8 |
| β-strand | 31-33 | 3 | 8 |
| α-helix | 34-43 | 10 | |
| β-strand | 48-49 | 2 | 9 |
| β-strand | 56-57 | 2 | 9 |
| β-strand | 65 | 1 | 8 |
| α-helix | 67-78 | 12 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin-conjugating enzyme E2 N | A, B | protein | 152 | Homo sapiens | P61088 (AlphaFold model) |
| Tripartite motif-containing 25 variant | F, G | protein | 86 | Homo sapiens | Q14258 (AlphaFold model) |
| Polyubiquitin-B | C, D | protein | 76 | Homo sapiens | P0CG47 (AlphaFold model) |
Sequence of entity 1 (A, B), FASTA
>5EYA_1 Ubiquitin-conjugating enzyme E2 N (chains A, B)
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
EYPMAAPKVRFMTKIYHPNVDKLGRIKLDILKDKWSPALQIRTVLLSIQALLSAPNPDDP
LANDVAEQWKTNEAQAIETARAWTRLYAMNNI
Sequence of entity 2 (F, G), FASTA
>5EYA_2 Tripartite motif-containing 25 variant (chains F, G)
GSHMAELCPLAEELSCSICLEPFKEPVTTPCGHNFCGSCLNETWAVQGSPYLCPQCRAVY
QARPQLHKNTVLCNVVEQFLQADLAR
Sequence of entity 3 (C, D), FASTA
>5EYA_3 Polyubiquitin-B (chains C, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Mechanism of TRIM25 Catalytic Activation in the Antiviral RIG-I Pathway. Sanchez, J.G., Chiang, J.J., Sparrer, K.M. et al. Cell Rep (2016) 16:1315-1325. DOI 10.1016/j.celrep.2016.06.070 · PubMed
Other PDB entries of the same protein (UniProt P61088 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4ONL 1.35 Å, Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P
- 4ONM 1.35 Å, Crystal structure of human Mms2/Ubc13 - NSC697923
- 5YWR 1.47 Å, Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13)
- 4ONN 1.5 Å, Crystal structure of human Mms2/Ubc13 - BAY 11-7082
- 9BIV 1.68 Å, Crystal Structure of Ubc13 with a New Active Site Loop Conformation
- 9LHJ 1.68 Å, UBE2N/UBE2V2 complexed with a covalent inhibitor
- 4DHI 1.8 Å, Structure of C. elegans OTUB1 bound to human UBC13
- 4NR3 1.8 Å, Crystal Structure of a human Mms2/Ubc13 L121G mutant
- 1J7D 1.85 Å, Crystal Structure of hMms2-hUbc13
- 4NRG 1.95 Å, Crystal Structure of a human Mms2/Ubc13 D118G mutant
- 6ULH 1.97 Å, Structure of MavC in complex with its substrate in R3 spacegroup
- 4TKP 2.08 Å, Complex of Ubc13 with the RING domain of the TRIM5alpha retroviral restriction factor
Browse structure collections
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