7YV4: Human UCHL3

Crystal structure of human UCHL3 in complex with Farrerol. Determined by X-ray diffraction at 1.58 Å resolution. Released 19 Apr 2023.

Method: X-ray diffraction
Resolution: 1.58 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,906
Mol. weight: 26.51 kDa
Ligands: JXY
Released: 19 Apr 2023

Explore 7YV4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YV4 contains 10 α-helices and 8 β-strands across 1 chain. 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	25	1	1
β-strand	29-34	6	2
α-helix	39-42	4
β-strand	49-56	8	2
α-helix	60-76	17
α-helix	92-94	3
α-helix	95-105	11
α-helix	108-110	3
β-strand	113	1	1
α-helix	118-126	9
α-helix	131-140	10
α-helix	142-144	3
β-strand	169-176	8	2
β-strand	179-183	5	2
β-strand	191-195	5	2
α-helix	201-213	13
β-strand	224-229	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase isozyme L3	A	protein	230	Homo sapiens	P15374 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7YV4_1 Ubiquitin carboxyl-terminal hydrolase isozyme L3 (chains A)
MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITE
KYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLK
KFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHL
YELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA

Ligands and cofactors

ID	Name	Formula	Copies
JXY	(2~{S})-2-(4-hydroxyphenyl)-6,8-dimethyl-5,7-bis(oxidanyl)-2,3-dihydrochromen-4…	C17 H16 O5	1

Primary citation

Farrerol directly activates the deubiqutinase UCHL3 to promote DNA repair and reprogramming when mediated by somatic cell nuclear transfer. Zhang, W., Wang, M., Song, Z. et al. Nat Commun (2023) 14:1838-1838. DOI 10.1038/s41467-023-37576-9 · PubMed

Other PDB entries of the same protein (UniProt P15374 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
1UCH 1.8 Å, Deubiquitinating enzyme uch-L3 (HUMAN) at 1.8 Å resolution
13DF 1.84 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(3-methoxyphenyl)benzamid…
6ISU 1.87 Å, Crystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting…
13CV 1.94 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(pyridin-2-yl)benzamide…
13CU 1.95 Å, Crystal structure of covalent inhibitor 2-chloro-N-(3-((pyridin-2-ylthio)methyl)phenyl)ac…
6QML 2.1 Å, UCHL3 in complex with synthetic, K27-linked diubiquitin
13CW 2.48 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(m-tolyl)benzamide bound…
35YH 2.6 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(3-hydroxyphenyl)benzamid…

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