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 
  • R-Value Observed: 0.197 

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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
  • Primary Citation of Related Structures:  
    5LSO

  • 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 (ULM) peptide sequences plays important roles during early steps of spliceosome assembly ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 45A, C [auth B]103Homo sapiensMutation(s): 0 
Gene Names: RBM17SPF45
Find proteins for Q96I25 (Homo sapiens)
Explore Q96I25 
Go to UniProtKB:  Q96I25
NIH Common Fund Data Resources
PHAROS:  Q96I25
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LYS-SER-ARG-TRP-ASP-GLUB [auth C], D6Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.6α = 90
b = 73.59β = 97.9
c = 45.01γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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