2LKR | pdb_00002lkr

Yeast U2/U6 complex

• PDB DOI: https://doi.org/10.2210/pdb2LKR/pdb
• BMRB: 17961
• NAKB: 2LKR

• Classification: RNA
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2011-10-19 Released: 2012-02-22 
• Deposition Author(s): Burke, J.E., Sashital, D.G., Zuo, X., Wang, Y., 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 of the yeast U2/U6 snRNA complex.

Burke, J.E., Sashital, D.G., Zuo, X., Wang, Y.X., Butcher, S.E.

(2012) RNA 18: 673-683

• PubMed: 22328579 
• DOI: https://doi.org/10.1261/rna.031138.111
• Primary Citation Related Structures: 
  2LK3, 2LKR


• PubMed Abstract: 
  

  The U2/U6 snRNA complex is a conserved and essential component of the active spliceosome that interacts with the pre-mRNA substrate and essential protein splicing factors to promote splicing catalysis. Here we have elucidated the solution structure of a 111-nucleotide U2/U6 complex using an approach that integrates SAXS, NMR, and molecular modeling. The U2/U6 structure contains a three-helix junction that forms an extended "Y" shape. The U6 internal stem-loop (ISL) forms a continuous stack with U2/U6 Helices Ib, Ia, and III. The coaxial stacking of Helix Ib on the U6 ISL is a configuration that is similar to the Domain V structure in group II introns. Interestingly, essential features of the complex--including the U80 metal binding site, AGC triad, and pre-mRNA recognition sites--localize to one face of the molecule. This observation suggests that the U2/U6 structure is well-suited for orienting substrate and cofactors during splicing catalysis.

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.56 kDa 
• Atom Count: 2,350 
• Modeled Residue Count: 111 
• Deposited Residue Count: 111 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (111-MER)	A	111	Saccharomyces cerevisiae

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: 2012-02-22 
Deposition Author(s): Burke, J.E., Sashital, D.G., Zuo, X., Wang, Y., Butcher, S.E.

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references