7YV4

Crystal structure of human UCHL3 in complex with Farrerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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.Fu, Q.Chen, J.Zhang, W.Gao, S.Sun, X.Yang, G.Zhang, Q.Yang, J.Tang, H.Wang, H.Kou, X.Wang, H.Mao, Z.Xu, X.Gao, S.Jiang, Y.

(2023) Nat Commun 14: 1838-1838

  • DOI: https://doi.org/10.1038/s41467-023-37576-9
  • Primary Citation of Related Structures:  
    7YV4

  • PubMed Abstract: 

    Farrerol, a natural flavanone, promotes homologous recombination (HR) repair to improve genome-editing efficiency, but the specific protein that farrerol directly targets to regulate HR repair and the underlying molecular mechanisms have not been determined. Here, we find that the deubiquitinase UCHL3 is the direct target of farrerol. Mechanistically, farrerol enhanced the deubiquitinase activity of UCHL3 to promote RAD51 deubiquitination, thereby improving HR repair. Importantly, we find that embryos of somatic cell nuclear transfer (SCNT) exhibited defective HR repair, increased genomic instability and aneuploidy, and that the farrerol treatment post nuclear transfer enhances HR repair, restores transcriptional and epigenetic network, and promotes SCNT embryo development. Ablating UCHL3 significantly attenuates farrerol-mediated stimulation in HR and SCNT embryo development. In summary, we identify farrerol as an activator of the deubiquitinase UCHL3, highlighted the importance of HR and epigenetic changes in SCNT reprogramming and provide a feasible method to promote SCNT efficiency.


  • Organizational Affiliation

    Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase isozyme L3230Homo sapiensMutation(s): 0 
Gene Names: UCHL3
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P15374 (Homo sapiens)
Explore P15374 
Go to UniProtKB:  P15374
PHAROS:  P15374
GTEx:  ENSG00000118939 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15374
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JXY (Subject of Investigation/LOI)
Query on JXY

Download Ideal Coordinates CCD File 
B [auth A](2~{S})-2-(4-hydroxyphenyl)-6,8-dimethyl-5,7-bis(oxidanyl)-2,3-dihydrochromen-4-one
C17 H16 O5
DYHOLQACRGJEHX-ZDUSSCGKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.054α = 90
b = 63.873β = 90
c = 77.161γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82071565
National Natural Science Foundation of China (NSFC)China81972457
National Natural Science Foundation of China (NSFC)China32171288
National Natural Science Foundation of China (NSFC)China81973500
National Natural Science Foundation of China (NSFC)China31721003
National Natural Science Foundation of China (NSFC)China31820103009
National Natural Science Foundation of China (NSFC)China31871446
National Natural Science Foundation of China (NSFC)China32070857

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description