8C0D: UFL1/DDRGK1
UFL1/DDRGK1 bound to UFC1. Determined by X-ray diffraction at 2.56 Å resolution. Released 27 Dec 2023.
- Method
- X-ray diffraction
- Resolution
- 2.56 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 6,518
- Mol. weight
- 108.19 kDa
- Released
- 27 Dec 2023
Explore 8C0D in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8C0D contains 52 α-helices and 32 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: 11 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1-20 | 20 | |
| α-helix | 22-25 | 4 | |
| α-helix | 29-41 | 13 | |
| β-strand | 48-49 | 2 | 1 |
| β-strand | 55-57 | 3 | 1 |
| α-helix | 59-73 | 15 | |
| β-strand | 76-78 | 3 | 2 |
| α-helix | 79-81 | 3 | |
| α-helix | 82-86 | 5 | |
| α-helix | 90-94 | 5 | |
| α-helix | 97-104 | 8 | |
| β-strand | 107-110 | 4 | 2 |
| β-strand | 113-116 | 4 | 2 |
| α-helix | 117-131 | 15 | |
| α-helix | 139-145 | 7 | |
| α-helix | 150-158 | 9 | |
Chain B: 6 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 206-208 | 3 | |
| α-helix | 209-226 | 18 | |
| β-strand | 228-230 | 3 | 3 |
| α-helix | 231-238 | 8 | |
| α-helix | 242-255 | 14 | |
| β-strand | 261-262 | 2 | 3 |
| β-strand | 267-269 | 3 | 3 |
| α-helix | 273-286 | 14 | |
| β-strand | 288-290 | 3 | 1 |
| α-helix | 291-301 | 11 | |
Chain C: 10 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-12 | 7 | |
| α-helix | 14-15 | 2 | |
| α-helix | 28-48 | 21 | |
| β-strand | 54-58 | 5 | 4 |
| β-strand | 64-73 | 10 | 4 |
| β-strand | 76-85 | 10 | 4 |
| α-helix | 86-87 | 2 | |
| α-helix | 94-95 | 2 | |
| β-strand | 98 | 1 | 4 |
| α-helix | 100-102 | 3 | |
| β-strand | 109 | 1 | 5 |
| β-strand | 114 | 1 | 4 |
| β-strand | 115 | 1 | 5 |
| α-helix | 121-127 | 7 | |
| α-helix | 134-137 | 4 | |
| α-helix | 138-142 | 5 | |
| α-helix | 143-155 | 13 | |
Chain D: 11 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1-20 | 20 | |
| α-helix | 22-25 | 4 | |
| α-helix | 29-41 | 13 | |
| β-strand | 48-49 | 2 | 6 |
| β-strand | 55-57 | 3 | 6 |
| α-helix | 59-73 | 15 | |
| β-strand | 76-78 | 3 | 7 |
| α-helix | 79-81 | 3 | |
| α-helix | 82-86 | 5 | |
| α-helix | 90-94 | 5 | |
| α-helix | 97-104 | 8 | |
| β-strand | 107-110 | 4 | 7 |
| β-strand | 113-116 | 4 | 7 |
| α-helix | 117-128 | 12 | |
| α-helix | 140-145 | 6 | |
| α-helix | 150-158 | 9 | |
Chain E: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 215-226 | 12 | |
| β-strand | 228-230 | 3 | 8 |
| α-helix | 231-238 | 8 | |
| α-helix | 242-255 | 14 | |
| β-strand | 261-262 | 2 | 8 |
| β-strand | 267-269 | 3 | 8 |
| α-helix | 273-286 | 14 | |
| β-strand | 288-290 | 3 | 6 |
| α-helix | 291-301 | 11 | |
Chain F: 9 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-12 | 7 | |
| α-helix | 14-15 | 2 | |
| α-helix | 28-48 | 21 | |
| β-strand | 54-58 | 5 | 9 |
| β-strand | 64-73 | 10 | 9 |
| β-strand | 76-85 | 10 | 9 |
| α-helix | 94-95 | 2 | |
| β-strand | 98 | 1 | 9 |
| α-helix | 100-102 | 3 | |
| β-strand | 109 | 1 | 10 |
| β-strand | 114 | 1 | 9 |
| β-strand | 115 | 1 | 10 |
| α-helix | 121-127 | 7 | |
| α-helix | 134-137 | 4 | |
| α-helix | 138-142 | 5 | |
| α-helix | 143-155 | 13 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| E3 UFM1-protein ligase 1 | A, D | protein | 194 | Homo sapiens | O94874 (AlphaFold model) |
| DDRGK domain-containing protein 1 | B, E | protein | 110 | Homo sapiens | Q96HY6 (AlphaFold model) |
| Ubiquitin-fold modifier-conjugating enzyme 1 | C, F | protein | 168 | Homo sapiens | Q9Y3C8 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>8C0D_1 E3 UFM1-protein ligase 1 (chains A, D)
MGHHHHHHENLYFQGMADAWEEIRRLAADFQRAQFAEATQRLSERNCIEIVNKLIAQKQL
EVVHTLDGKEYITPAQISKEMRDELHVRGGRVNIVDLQQVINVDLIHIENRIGDIIKSEK
HVQLVLGQLIDENYLDRLAEEVNDKLQESGQVTISELCKTYDLPGNFLTQALTQRLGRII
SGHIDLDNRGVIFT
Sequence of entity 2 (B, E), FASTA
>8C0D_2 DDRGK domain-containing protein 1 (chains B, E)
ETMTEEQSQSFLTEFINYIKQSKVVLLEDLASQVGLRTQDTINRIQDLLAEGTITGVIDD
RGKFIYITPEELAAVANFIRQRGRVSIAELAQASNSLIAWGRESPAQAPA
Sequence of entity 3 (C, F), FASTA
>8C0D_3 Ubiquitin-fold modifier-conjugating enzyme 1 (chains C, F)
MADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNK
EGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKIKLTDH
FKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHKEKCNQG
Primary citation
The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons. Makhlouf, L., Peter, J.J., Magnussen, H.M. et al. Nature (2024) 627:437-444. DOI 10.1038/s41586-024-07093-w · PubMed
Other PDB entries of the same protein (UniProt O94874 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8QFD 2.2 Å, UFL1 E3 ligase bound 60S ribosome
- 8OJ5 2.9 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution)
- 9GY4 3.0 Å, 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF…
- 8B9X 3.07 Å, Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1
- 8OHD 3.1 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native)
- 8QFC 3.2 Å, UFL1 E3 ligase bound 60S ribosome
- 8OJ0 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native)
- 8OJ8 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native)
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