9FJ4: Ubiquitin

Structure of ubiquitin bound to coiled coil-UIM form 1. Determined by X-ray diffraction at 1.54 Å resolution. Released 18 Sept 2024.

Method: X-ray diffraction
Resolution: 1.54 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 949
Mol. weight: 13.67 kDa
Ligands: A1IDH
Released: 18 Sept 2024

Explore 9FJ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FJ4 contains 5 α-helices and 7 β-strands across 3 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	2-7	6	1
β-strand	12-16	5	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	0-14	15

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-18	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyubiquitin-C	A	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	protein	20	synthetic construct
Lys-gln-lys-ile-ala-ala-leu-lys-tyr-lys-ile-ala-ala-leu-lys-gln-lys-ile-gln	C	protein	20	synthetic construct

Sequence of entity 1 (A), FASTA

>9FJ4_1 Polyubiquitin-C (chains A)
GSGGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGG

Sequence of entity 2 (B), FASTA

>9FJ4_2 GLU-GLN-GLU-ILE-GLU-GLU-LEU-GLU-ILE-GLU-ILE-ALA-ILE-LEU-LEU-SER-GLU-ILE-GLU-GLY (chains B)
EQEIEELEIEIAILLSEIEG

Sequence of entity 3 (C), FASTA

>9FJ4_3 LYS-GLN-LYS-ILE-ALA-ALA-LEU-LYS-TYR-LYS-ILE-ALA-ALA-LEU-LYS-GLN-LYS-ILE-GLN (chains C)
KQKIAALKYKIAALKQKIQG

Ligands and cofactors

ID	Name	Formula	Copies
A1IDH	3-[1-(2-oxidanylideneethyl)-1,2,3-triazol-4-yl]propanal	C7 H9 N3 O4	1

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
9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
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

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