2GHP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2007.01.078
  • Primary Citation of Related Structures:  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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U4/U6 snRNA-associated splicing factor PRP24
A, B, C, D, E, F, G, H
292Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRP24
Find proteins for P49960 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49960
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 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 = 90.00
b = 125.848β = 90.00
c = 196.542γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
ARP/wARPmodel building
SCALEPACKdata scaling
PHENIXphasing
SHELXDphasing
RESOLVEphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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