9Q9O | pdb_00009q9o

TRIM21 PRYSPRY bound to compound 36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.368 (Depositor) 
  • R-Value Work: 
    0.302 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

State-selective small molecule degraders that preferentially remove aggregates and oligomers.

Luptak, J.Clift, D.Mukadam, A.Benn, J.Rhinesmith, T.McLaughlin, S.H.Dodds, A.C.Lapetaje, J.E.Sczaniecka-Clift, M.France, D.J.McEwan, W.A.James, L.C.

(2025) Nat Commun 16: 10486-10486

  • DOI: https://doi.org/10.1038/s41467-025-65454-z
  • Primary Citation Related Structures: 
    9Q9O, 9Q9P, 9Q9Q, 9Q9R, 9R40

  • PubMed Abstract: 

    TRIM21 is a unique E3 ligase that uses a clustering-based activation mechanism to degrade complex multimeric substrates. This activity underpins the targeted protein degradation technology Trim-Away and genetically encoded degraders that selectively target aggregated tau protein and prevent tauopathy. Here we describe small molecules that mimic TRIM21's natural epitope and function as either effective inhibitors or potent and selective degraders called TRIMTACs. TRIMTACs mediate degradation as rapidly as PROTACs but can also selectively degrade specific protein pools depending on assembly state. We demonstrate the utility of this state-specific degradation by selectively removing the pro-inflammatory signalling protein Myd88 when assembled into the Myddosome and the cell-death protein RIPK3 when polymerised into the Necrosome. We further show that TRIMTACs can inhibit seeded tau aggregation under conditions where a PROTAC is ineffective. These results highlight that TRIM21's clustering-based activation can be exploited by small molecule degraders to carry out state-selective degradation of therapeutic targets.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 92.16 kDa 
  • Atom Count: 6,064 
  • Modeled Residue Count: 732 
  • Deposited Residue Count: 792 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase TRIM21A [auth B],
B [auth A],
C,
D
198Homo sapiensMutation(s): 0 
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.368 (Depositor) 
  • R-Value Work:  0.302 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.685α = 90
b = 74.38β = 90.103
c = 90.109γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-10-08 
  • Deposition Author(s): Luptak, J.

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references