1LPW

Solution structure of the yeast spliceosomal U2 snRNA-intron branch site helix featuring a conserved pseudouridine

• PDB DOI: https://doi.org/10.2210/pdb1LPW/pdb
• BMRB: 5394
• NAKB: 1LPW

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


• Deposited: 2002-05-08 Released: 2002-11-27 
• Deposition Author(s): Newby, M.I., Greenbaum, N.L.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 800 
• Conformers Submitted: 9 
• Selection Criteria: lowest energy structures that did not violate data from fluorescence experiments 

Literature

Sculpting of the Spliceosomal Branch Site Recognition Motif by a Conserved Pseudouridine

Newby, M.I., Greenbaum, N.L.

(2002) Nat Struct Biol 12: 958-965

• PubMed: 12426583 
• DOI: https://doi.org/10.1038/nsb873
• Primary Citation of Related Structures:  
  1LMV, 1LPW


• PubMed Abstract: 
  

  Pairing of a consensus sequence of the precursor (pre)-mRNA intron with a short region of the U2 small nuclear (sn)RNA during assembly of the eukaryotic spliceosome results in formation of a complementary helix of seven base pairs with a single unpaired adenosine residue. The 2' OH of this adenosine, called the branch site, brings about nucleophilic attack at the pre-mRNA 5' splice site in the first step of splicing. Another feature of this pairing is the phylogenetic conservation of a pseudouridine (psi) residue in U2 snRNA nearly opposite the branch site. We show that the presence of this psi in the pre-mRNA branch-site helix of Saccharomyces cerevisiae induces a dramatically altered architectural landscape compared with that of its unmodified counterpart. The psi-induced structure places the nucleophile in an accessible position for the first step of splicing.

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Organizational Affiliation: 

Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-4390, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.02 kDa 
• Atom Count: 398 
• Modelled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*UP*GP*(PSU)P*AP*GP*UP*A)-3'	A	9	Saccharomyces cerevisiae

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*UP*AP*CP*UP*AP*AP*CP*AP*CP*C)-3'	B	10	Saccharomyces cerevisiae

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 800 
• Conformers Submitted: 9 
• Selection Criteria: lowest energy structures that did not violate data from fluorescence experiments 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-27 
Deposition Author(s): Newby, M.I., Greenbaum, N.L.

Revision History  

• Version 1.0: 2002-11-27
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection