8Y5B

Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (R)-hydroxyl-acepromazine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


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Literature

Selective degradation of multimeric proteins by TRIM21-based molecular glue and PROTAC degraders.

Lu, P.Cheng, Y.Xue, L.Ren, X.Xu, X.Chen, C.Cao, L.Li, J.Wu, Q.Sun, S.Hou, J.Jia, W.Wang, W.Ma, Y.Jiang, Z.Li, C.Qi, X.Huang, N.Han, T.

(2024) Cell 

  • DOI: https://doi.org/10.1016/j.cell.2024.10.015
  • Primary Citation of Related Structures:  
    8Y58, 8Y59, 8Y5B

  • PubMed Abstract: 

    Targeted protein degradation (TPD) utilizes molecular glues or proteolysis-targeting chimeras (PROTACs) to eliminate disease-causing proteins by promoting their interaction with E3 ubiquitin ligases. Current TPD approaches are limited by reliance on a small number of constitutively active E3 ubiquitin ligases. Here, we report that (S)-ACE-OH, a metabolite of the antipsychotic drug acepromazine, acts as a molecular glue to induce an interaction between the E3 ubiquitin ligase TRIM21 and the nucleoporin NUP98, leading to the degradation of nuclear pore proteins and disruption of nucleocytoplasmic trafficking. Functionalization of acepromazine into PROTACs enabled selective degradation of multimeric proteins, such as those within biomolecular condensates, while sparing monomeric proteins. This selectivity is consistent with the requirement of substrate-induced clustering for TRIM21 activation. As aberrant protein assemblies cause diseases such as autoimmunity, neurodegeneration, and cancer, our findings highlight the potential of TRIM21-based multimer-selective degraders as a strategy to tackle the direct causes of these diseases.


  • Organizational Affiliation

    Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase TRIM21192Homo sapiensMutation(s): 1 
Gene Names: TRIM21RNF81RO52SSA1
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P19474 (Homo sapiens)
Explore P19474 
Go to UniProtKB:  P19474
PHAROS:  P19474
GTEx:  ENSG00000132109 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19474
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D5Z (Subject of Investigation/LOI)
Query on A1D5Z

Download Ideal Coordinates CCD File 
B [auth A](1~{R})-1-[10-[3-(dimethylamino)propyl]phenothiazin-2-yl]ethanol
C19 H24 N2 O S
ZIJWCRNUEBJMSQ-CQSZACIVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.889α = 90
b = 100.889β = 90
c = 48.194γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaZ201100005320010
Other governmentChinaZ221100007022004

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references