9FJ3: Ubiquitin bound of coiled-coil UIM form 2
Structure of ubiquitin bound of coiled-coil UIM form 2. Determined by X-ray diffraction at 1.4 Å resolution. Released 18 Sept 2024.
- Method
- X-ray diffraction
- Resolution
- 1.4 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 6
- Atoms
- 2,051
- Mol. weight
- 27.34 kDa
- Ligands
- A1IDH
- Released
- 18 Sept 2024
Explore 9FJ3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9FJ3 contains 11 α-helices and 14 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: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1-6 | 6 | 1 |
| β-strand | 12-17 | 6 | 1 |
| β-strand | 22 | 1 | 2 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 1 |
| β-strand | 48-49 | 2 | 1 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 2 |
| β-strand | 66-71 | 6 | 1 |
Chain B: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 0-16 | 17 | |
Chain C: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-17 | 16 | |
Chain D: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1-6 | 6 | 3 |
| β-strand | 12-17 | 6 | 3 |
| β-strand | 22 | 1 | 4 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 3 |
| β-strand | 48-49 | 2 | 3 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 4 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 3 |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 0-17 | 18 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-19 | 18 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Polyubiquitin-C | A, D | protein | 81 | Homo sapiens | P0CG48 (AlphaFold model) |
| Glu-gln-glu-ile-glu-glu-leu-glu-ile-glu-ile-ala-ile-leu-leu-ser-glu-ile-glu-gly | B, E | protein | 20 | synthetic construct | |
| Lys-gln-lys-ile-ala-ala-leu-lys-tyr-lys-ile-ala-ala-leu-lys-gln-lys-ile | C, F | protein | 20 | synthetic construct | |
Sequence of entity 1 (A, D), FASTA
>9FJ3_1 Polyubiquitin-C (chains A, D)
GSGGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGG
Sequence of entity 2 (B, E), FASTA
>9FJ3_2 GLU-GLN-GLU-ILE-GLU-GLU-LEU-GLU-ILE-GLU-ILE-ALA-ILE-LEU-LEU-SER-GLU-ILE-GLU-GLY (chains B, E)
EQEIEELEIEIAILLSEIEG
Sequence of entity 3 (C, F), FASTA
>9FJ3_3 LYS-GLN-LYS-ILE-ALA-ALA-LEU-LYS-TYR-LYS-ILE-ALA-ALA-LEU-LYS-GLN-LYS-ILE (chains C, F)
KQKIAALKYKIAALKQKIQG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| A1IDH | 3-[1-(2-oxidanylideneethyl)-1,2,3-triazol-4-yl]propanal | C7 H9 N3 O4 | 2 |
Primary citation
An engineered ubiquitin binding coiled coil peptide. Vosbein, P., Vergara, P.P., Huang, D.T. et al. Chem Sci (2024) 15:15776-15782. DOI 10.1039/d4sc04204b · PubMed
Other PDB entries of the same protein (UniProt P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
- 1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
- 5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
- 2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
- 4HK2 1.4 Å, U7Ub25.2540
- 1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
- 4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
- 7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
- 5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
- 9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
- 9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant
- 4UN2 1.51 Å, Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin
Browse structure collections
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