1XHP | pdb_00001xhp

Solution Structure of the Extended U6 ISL as Observed in the U2/U6 complex from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb1XHP/pdb
• BMRB: 6320
• NAKB: 1XHP

• Classification: RNA
• Mutation(s): No 


• Deposited: 2004-09-20 Released: 2004-11-23 
• Deposition Author(s): Sashital, D.G., Cornilescu, G., 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

U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction

Sashital, D.G., Cornilescu, G., McManus, C.J., Brow, D.A., Butcher, S.E.

(2004) Nat Struct Mol Biol 11: 1237-1242

• PubMed: 15543154 
• DOI: https://doi.org/10.1038/nsmb863
• Primary Citation of Related Structures:  
  1XHP


• PubMed Abstract: 
  

  Intron removal in nuclear precursor mRNA is catalyzed through two transesterification reactions by a multi-megaDalton ribonucleoprotein machine called the spliceosome. A complex between U2 and U6 small nuclear RNAs is a core component of the spliceosome. Here we present an NMR structural analysis of a protein-free U2-U6 complex from Saccharomyces cerevisiae. The observed folding of the U2-U6 complex is a four-helix junction, in which the catalytically important AGC triad base-pairs only within U6 and not with U2. The base-pairing of the AGC triad extends the U6 intramolecular stem-loop (U6 ISL), and the NMR structure of this extended U6 ISL reveals structural similarities with domain 5 of group II self-splicing introns. The observed conformation of the four-helix junction could be relevant to the first, but not the second, step of splicing and may help to position the U6 ISL adjacent to the 5' splice site.

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Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.24 kDa 
• Atom Count: 677 
• Modeled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
U6 snRNA	A	32	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: 2004-11-23 
Deposition Author(s): Sashital, D.G., Cornilescu, G., Butcher, S.E.

Revision History  

• Version 1.0: 2004-11-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection