Crystal structure of PUF60 UHM domain in complex with 7,8 dimethoxyperphenazine

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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Identification of phenothiazine derivatives as UHM-binding inhibitors of early spliceosome assembly.

Jagtap, P.K.A.Kubelka, T.Soni, K.Will, C.L.Garg, D.Sippel, C.Kapp, T.G.Potukuchi, H.K.Schorpp, K.Hadian, K.Kessler, H.Luhrmann, R.Hausch, F.Bach, T.Sattler, M.

(2020) Nat Commun 11: 5621-5621

  • DOI: https://doi.org/10.1038/s41467-020-19514-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Interactions between U2AF homology motifs (UHMs) and U2AF ligand motifs (ULMs) play a crucial role in early spliceosome assembly in eukaryotic gene regulation. UHM-ULM interactions mediate heterodimerization of the constitutive splicing factors U2AF65 and U2AF35 and between other splicing factors that regulate spliceosome assembly at the 3' splice site, where UHM domains of alternative splicing factors, such as SPF45 and PUF60, contribute to alternative splicing regulation. Here, we performed high-throughput screening using fluorescence polarization assays with hit validation by NMR and identified phenothiazines as general inhibitors of UHM-ULM interactions. NMR studies show that these compounds occupy the tryptophan binding pocket of UHM domains. Co-crystal structures of the inhibitors with the PUF60 UHM domain and medicinal chemistry provide structure-activity-relationships and reveal functional groups important for binding. These inhibitors inhibit early spliceosome assembly on pre-mRNA substrates in vitro. Our data show that spliceosome assembly can be inhibited by targeting UHM-ULM interactions by small molecules, thus extending the toolkit of splicing modulators for structural and biochemical studies of the spliceosome and splicing regulation.

  • Organizational Affiliation

    Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. sattler@helmholtz-muenchen.de.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin,Poly(U)-binding-splicing factor PUF60
A, B, C, D
222Citrobacter freundii MGH 56Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: AF42_05360PUF60FIRROBPISIAHBP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHX1 (Homo sapiens)
Explore Q9UHX1 
Go to UniProtKB:  Q9UHX1
GTEx:  ENSG00000179950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHX1
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LJT Binding MOAD:  6SLO IC50: 1.78e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.52α = 90
b = 89.4β = 90
c = 149.21γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description