4AP4: Rnf4 - ubch5a - ubiquitin heterotrimeric complex
Rnf4 - ubch5a - ubiquitin heterotrimeric complex. Determined by X-ray diffraction at 2.21 Å resolution. Released 25 Jul 2012.
- Method
- X-ray diffraction
- Resolution
- 2.21 Å
- Organisms
- RATTUS NORVEGICUS, HOMO SAPIENS
- Chains
- 5
- Atoms
- 4,748
- Mol. weight
- 67.08 kDa
- Ligands
- ZN
- Released
- 25 Jul 2012
Explore 4AP4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4AP4 contains 26 α-helices and 48 β-strands across 5 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: 5 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 135 | 1 | 1 |
| β-strand | 142 | 1 | 1 |
| α-helix | 143-148 | 6 | |
| β-strand | 153-156 | 4 | 2 |
| β-strand | 161-163 | 3 | 2 |
| α-helix | 164-171 | 8 | |
| β-strand | 176 | 1 | 3 |
| β-strand | 183 | 1 | 3 |
| β-strand | 189-191 | 3 | 2 |
| β-strand | 193 | 1 | 4 |
| β-strand | 200 | 1 | 5 |
| β-strand | 207 | 1 | 5 |
| α-helix | 208-213 | 6 | |
| β-strand | 218-221 | 4 | 6 |
| β-strand | 225 | 1 | 4 |
| β-strand | 226-228 | 3 | 6 |
| α-helix | 229-238 | 10 | |
| β-strand | 241 | 1 | 7 |
| β-strand | 248 | 1 | 7 |
| α-helix | 251-253 | 3 | |
| β-strand | 254-257 | 4 | 6 |
Chain B: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 0-15 | 16 | |
| β-strand | 21-25 | 5 | 8 |
| β-strand | 32-38 | 7 | 8 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 8 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 8 |
| β-strand | 78 | 1 | 9 |
| β-strand | 83 | 1 | 8 |
| β-strand | 84 | 1 | 9 |
| β-strand | 86 | 1 | 10 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-110 | 12 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-145 | 15 | |
Chain C: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 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 |
| β-strand | 55 | 1 | 12 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 11 |
| β-strand | 75 | 1 | 10 |
Chain E: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-15 | 14 | |
| β-strand | 21-25 | 5 | 13 |
| β-strand | 32-38 | 7 | 13 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 13 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 13 |
| β-strand | 78 | 1 | 14 |
| β-strand | 83 | 1 | 13 |
| β-strand | 84 | 1 | 14 |
| β-strand | 86 | 1 | 15 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-110 | 12 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-145 | 15 | |
Chain F: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1-6 | 6 | 16 |
| β-strand | 12-17 | 6 | 16 |
| β-strand | 22 | 1 | 17 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 16 |
| β-strand | 48-49 | 2 | 16 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 17 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 16 |
| β-strand | 75 | 1 | 15 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| E3 ubiquitin ligase RNF4 | A | protein | 133 | RATTUS NORVEGICUS | O88846 (AlphaFold model) |
| Ubiquitin-conjugating enzyme E2 D1 | B, E | protein | 153 | HOMO SAPIENS | P51668 (AlphaFold model) |
| Ubiquitin C | C, F | protein | 80 | HOMO SAPIENS | P0CG48 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>4AP4_1 E3 UBIQUITIN LIGASE RNF4 (chains A)
GAMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH
KRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR
KKINHKRYHPIYI
Sequence of entity 2 (B, E), FASTA
>4AP4_2 UBIQUITIN-CONJUGATING ENZYME E2 D1 (chains B, E)
GAGSGSMALKRIQKELSDLQRDPPAHCRAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTV
HFPTDYPFKPPKIAFTTKIYHPNINSNGSIKLDILRSQWSPALTVSKVLLSICSLLCDPN
PDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM
Sequence of entity 3 (C, F), FASTA
>4AP4_3 UBIQUITIN C (chains C, F)
GAMGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Structure of a Ring E3 Ligase and Ubiquitin-Loaded E2 Primed for Catalysis. Plechanovova, A., Jaffray, E., Tatham, M.H. et al. Nature (2012) 489:115. DOI 10.1038/NATURE11376 · PubMed
Other PDB entries of the same protein (UniProt O88846 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3NG2 1.8 Å, Crystal structure of the RNF4 ring domain dimer
- 5AIU 2.21 Å, A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink)
- 5AIT 3.4 Å, A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink)
Browse structure collections
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