1LMV

Solution structure of the unmodified U2 snRNA-intron branch site helix from S. cerevisiae


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 300 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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

Newby, M.I.Greenbaum, N.L.

(2002) Nat Struct Biol 9: 958-965

  • 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*GP*GP*UP*GP*UP*AP*GP*UP*A)-3'9Saccharomyces cerevisiae
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(*UP*AP*CP*UP*AP*AP*CP*AP*CP*C)-3'10Saccharomyces cerevisiae
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 300 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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