Crystal structure of the N-terminal 3 RNA binding domains of the yeast splicing factor Prp24

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 

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Structure and interactions of the first three RNA recognition motifs of splicing factor prp24.

Bae, E.Reiter, N.J.Bingman, C.A.Kwan, S.S.Lee, D.Phillips Jr., G.N.Butcher, S.E.Brow, D.A.

(2007) J Mol Biol 367: 1447-1458

  • DOI: https://doi.org/10.1016/j.jmb.2007.01.078
  • Primary Citation of Related Structures:  
    2GHP, 2GO9

  • PubMed Abstract: 

    The essential Saccharomyces cerevisiae pre-messenger RNA splicing protein 24 (Prp24) has four RNA recognition motifs (RRMs) and facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 is a component of the free U6 small nuclear ribonucleoprotein particle (snRNP) but not the U4/U6 bi-snRNP, and so is thought to be displaced from U6 by U4/U6 base-pairing. The interaction partners of each of the four RRMs of Prp24 and how these interactions direct U4/U6 pairing are not known. Here we report the crystal structure of the first three RRMs and the solution structure of the first two RRMs of Prp24. Strikingly, RRM 2 forms extensive inter-domain contacts with RRMs 1 and 3. These contacts occupy much of the canonical RNA-binding faces (beta-sheets) of RRMs 1 and 2, but leave the beta-sheet of RRM 3 exposed. Previously identified substitutions in Prp24 that suppress mutations in U4 and U6 spliceosomal RNAs cluster primarily in the beta-sheet of RRM 3, but also in a conserved loop of RRM 2. RNA binding assays and chemical shift mapping indicate that a large basic patch evident on the surface of RRMs 1 and 2 is part of a high affinity U6 RNA binding site. Our results suggest that Prp24 binds free U6 RNA primarily with RRMs 1 and 2, which may remodel the U6 secondary structure. The beta-sheet of RRM 3 then influences U4/U6 pairing through interaction with an unidentified ligand.

  • Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 snRNA-associated splicing factor PRP24
A, B, C, D, E
A, B, C, D, E, F, G, H
292Saccharomyces cerevisiaeMutation(s): 5 
Gene Names: PRP24
Find proteins for P49960 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49960 
Go to UniProtKB:  P49960
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49960
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.608α = 90
b = 125.848β = 90
c = 196.542γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ARP/wARPmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-01-15
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description