9Q8Y: RNF38 RING with linchpin mutant R454Y
Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub. Determined by X-ray diffraction at 2.63 Å resolution. Released 30 Jul 2025.
- Method
- X-ray diffraction
- Resolution
- 2.63 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 4,056
- Mol. weight
- 67.11 kDa
- Ligands
- ZN
- Released
- 30 Jul 2025
Explore 9Q8Y in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9Q8Y contains 21 α-helices and 34 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: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-15 | 13 | |
| β-strand | 21-25 | 5 | 1 |
| β-strand | 32-38 | 7 | 1 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 1 |
| β-strand | 66-69 | 4 | 1 |
| β-strand | 75 | 1 | 2 |
| β-strand | 78 | 1 | 2 |
| β-strand | 84 | 1 | 2 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-111 | 13 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-145 | 15 | |
Chain B: 7 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-15 | 13 | |
| β-strand | 21-25 | 5 | 3 |
| β-strand | 32-38 | 7 | 3 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 3 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 3 |
| β-strand | 75 | 1 | 4 |
| β-strand | 78 | 1 | 4 |
| β-strand | 84 | 1 | 4 |
| α-helix | 87-89 | 3 | |
| α-helix | 99-111 | 13 | |
| α-helix | 121-129 | 9 | |
| α-helix | 131-145 | 15 | |
Chain C: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 391-395 | 5 | |
| β-strand | 398-400 | 3 | 5 |
| β-strand | 412-413 | 2 | 6 |
| β-strand | 418-419 | 2 | 6 |
| α-helix | 420-421 | 2 | |
| β-strand | 425-428 | 4 | 5 |
| β-strand | 434-436 | 3 | 5 |
| α-helix | 441-446 | 6 | |
| β-strand | 449 | 1 | 7 |
| β-strand | 456 | 1 | 7 |
Chain D: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 398-400 | 3 | 8 |
| β-strand | 413 | 1 | 9 |
| β-strand | 418 | 1 | 9 |
| β-strand | 425-429 | 5 | 8 |
| β-strand | 433-436 | 4 | 8 |
| α-helix | 439-446 | 8 | |
Chain F: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 10 |
| β-strand | 14-16 | 3 | 10 |
| β-strand | 22 | 1 | 11 |
| α-helix | 23-33 | 11 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 12 |
| β-strand | 48-49 | 2 | 12 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 11 |
| α-helix | 56-59 | 4 | |
| β-strand | 66 | 1 | 10 |
| β-strand | 68-71 | 4 | 12 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin-conjugating enzyme E2 D2 | A, B | protein | 146 | Homo sapiens | P62837 (AlphaFold model) |
| Isoform 2 of E3 ubiquitin-protein ligase RNF38 | C, D | protein | 69 | Homo sapiens | Q9H0F5 (AlphaFold model) |
| Ubiquitin-40S ribosomal protein S27a | F, G | protein | 77 | Homo sapiens | P0CG48 (AlphaFold model) |
Sequence of entity 1 (A, B), FASTA
>9Q8Y_1 Ubiquitin-conjugating enzyme E2 D2 (chains A, B)
ALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYP
FKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVP
EIARIYKTDREKYNRIAREWTQKYAM
Sequence of entity 2 (C, D), FASTA
>9Q8Y_2 Isoform 2 of E3 ubiquitin-protein ligase RNF38 (chains C, D)
KADIEQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRT
CPICYADAS
Sequence of entity 3 (F, G), FASTA
>9Q8Y_3 Ubiquitin-40S ribosomal protein S27a (chains F, G)
SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY
NIQKESTLHLVLRLRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 4 |
Primary citation
Tuning ubiquitin transfer by RING E3 ubiquitin ligases through the linchpin residue. Nakasone, M.A., Buetow, L., Gabrielsen, M. et al. Life Sci Alliance (2025) 8. DOI 10.26508/lsa.202503394 · PubMed
Other PDB entries of the same protein (UniProt P62837 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9GLS 1.25 Å, Crystal Structure of Human UBCH5B C85E
- 2ESK 1.36 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
- 6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
- 2ESQ 1.44 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
- 2ESO 1.5 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
- 2ESP 1.52 Å, Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
- 4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
- 7AI0 1.56 Å, Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal…
- 5D1M 1.58 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
- 3L1Y 1.6 Å, Crystal structure of human UBC4 E2 conjugating enzyme
- 5D1L 1.62 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)
- 6HPR 1.7 Å, Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub
Browse structure collections
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