2KH9 | pdb_00002kh9

Solution structure of yeast Prp24-RRM2 bound to a fragment of U6 RNA

• PDB DOI: https://doi.org/10.2210/pdb2KH9/pdb
• BMRB: 16246
• BMRB: 16230
• BMRB: 16243
• NAKB: 2KH9
• BMRB: 16244

• Classification: SPLICING/RNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-27 Released: 2010-03-09 
• Deposition Author(s): Martin-Tumasz, S.A., Butcher, S.E.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structure and functional implications of a complex containing a segment of U6 RNA bound by a domain of Prp24.

Martin-Tumasz, S., Reiter, N.J., Brow, D.A., Butcher, S.E.

(2010) RNA 16: 792-804

• PubMed: 20181740 
• DOI: https://doi.org/10.1261/rna.1913310
• Primary Citation Related Structures: 
  2KH9


• PubMed Abstract: 
  

  U6 RNA plays a critical role in pre-mRNA splicing. Assembly of U6 into the spliceosome requires a significant structural rearrangement and base-pairing with U4 RNA. In the yeast Saccharomyces cerevisiae, this process requires the essential splicing factor Prp24. We present the characterization and structure of a complex containing one of Prp24's four RNA recognition motif (RRM) domains, RRM2, and a fragment of U6 RNA. NMR methods were used to identify the preferred U6 binding sequence of RRM2 (5'-GAGA-3'), measure the affinity of the interaction, and solve the structure of RRM2 bound to the hexaribonucleotide AGAGAU. Interdomain contacts observed between RRM2 and RRM3 in a crystal structure of the free protein are not detectable in solution. A structural model of RRM1 and RRM2 bound to a longer segment of U6 RNA is presented, and a partial mechanism for Prp24's annealing activity is proposed.

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Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.78 kDa 
• Atom Count: 830 
• Modeled Residue Count: 92 
• Deposited Residue Count: 98 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U4/U6 snRNA-associated-splicing factor PRP24	A	92	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PRP24, YMR268C, YM8156.10C
UniProt
Find proteins for P49960 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49960  Go to UniProtKB:  P49960

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*AP*GP*AP*GP*AP*U)-3'	B	6	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Martin-Tumasz, S.A., Butcher, S.E.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-05-22
  Changes: Data collection