5LSO

Crystal structure of SPF45 UHM domain with cyclic peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Rational Design of Cyclic Peptide Inhibitors of U2AF Homology Motif (UHM) Domains To Modulate Pre-mRNA Splicing.

Jagtap, P.K.Garg, D.Kapp, T.G.Will, C.L.Demmer, O.Luhrmann, R.Kessler, H.Sattler, M.

(2016) J. Med. Chem. 59: 10190-10197

  • DOI: 10.1021/acs.jmedchem.6b01118

  • PubMed Abstract: 
  • U2AF homology motifs (UHMs) are atypical RNA recognition motif domains that mediate critical protein-protein interactions during the regulation of alternative pre-mRNA splicing and other processes. The recognition of UHM domains by UHM ligand motif ( ...

    U2AF homology motifs (UHMs) are atypical RNA recognition motif domains that mediate critical protein-protein interactions during the regulation of alternative pre-mRNA splicing and other processes. The recognition of UHM domains by UHM ligand motif (ULM) peptide sequences plays important roles during early steps of spliceosome assembly. Splicing factor 45 kDa (SPF45) is an alternative splicing factor implicated in breast and lung cancers, and splicing regulation of apoptosis-linked pre-mRNAs by SPF45 was shown to depend on interactions between its UHM domain and ULM motifs in constitutive splicing factors. We have developed cyclic peptide inhibitors that target UHM domains. By screening a focused library of linear and cyclic peptides and performing structure-activity relationship analysis, we designed cyclic peptides with 4-fold improved binding affinity for the SPF45 UHM domain compared to native ULM ligands and 270-fold selectivity to discriminate UHM domains from alternative and constitutive splicing factors. These inhibitors are useful tools to modulate and dissect mechanisms of alternative splicing regulation.


    Organizational Affiliation

    Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany.,Institute for Advanced Study (IAS), Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.,Max Planck Institute for Biophysical Chemistry , Department of Cellular Biochemistry, Am Fassberg 11, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 45
A, B
103Homo sapiensMutation(s): 0 
Gene Names: RBM17 (SPF45)
Find proteins for Q96I25 (Homo sapiens)
Go to Gene View: RBM17
Go to UniProtKB:  Q96I25
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LYS-SER-ARG-TRP-ASP-GLU
C, D
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.600α = 90.00
b = 73.590β = 97.90
c = 45.010γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2019-02-20
    Type: Advisory, Data collection, Derived calculations