4U34

Crystal Structures of RNA Duplexes Containing 2-thio-Uridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

Crystal Structure Studies of RNA Duplexes Containing s(2)U:A and s(2)U:U Base Pairs.

Sheng, J.Larsen, A.Heuberger, B.D.Blain, J.C.Szostak, J.W.

(2014) J Am Chem Soc 136: 13916-13924

  • DOI: 10.1021/ja508015a
  • Primary Citation of Related Structures:  
    4U34, 4U35, 4U37, 4U38

  • PubMed Abstract: 
  • Structural studies of modified nucleobases in RNA duplexes are critical for developing a full understanding of the stability and specificity of RNA base pairing. 2-Thio-uridine (s(2)U) is a modified nucleobase found in certain tRNAs. Thermodynamic studies have evaluated the effects of s(2)U on base pairing in RNA, where it has been shown to stabilize U:A pairs and destabilize U:G wobble pairs ...

    Structural studies of modified nucleobases in RNA duplexes are critical for developing a full understanding of the stability and specificity of RNA base pairing. 2-Thio-uridine (s(2)U) is a modified nucleobase found in certain tRNAs. Thermodynamic studies have evaluated the effects of s(2)U on base pairing in RNA, where it has been shown to stabilize U:A pairs and destabilize U:G wobble pairs. Surprisingly, no high-resolution crystal structures of s(2)U-containing RNA duplexes have yet been reported. We present here two high-resolution crystal structures of heptamer RNA duplexes (5'-uagcs(2)Ucc-3' paired with 3'-aucgAgg-5' and with 3'-aucgUgg-5') containing s(2)U:A and s(2)U:U pairs, respectively. For comparison, we also present the structures of their native counterparts solved under identical conditions. We found that replacing O2 with S2 stabilizes the U:A base pair without any detectable structural perturbation. In contrast, an s(2)U:U base pair is strongly stabilized in one specific U:U pairing conformation out of four observed for the native U:U base pair. This s(2)U:U stabilization appears to be due at least in part to an unexpected sulfur-mediated hydrogen bond. This work provides additional insights into the effects of 2-thio-uridine on RNA base pairing.


    Organizational Affiliation

    Howard Hughes Medical Institute, Center for Computational and Integrative Biology, and Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital , Boston, Massachusetts 02114, United States.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*AP*GP*CP*(SUR)P*CP*C-3')A7synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3')B7synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.35 Å
      • R-Value Free: 0.198 
      • R-Value Work: 0.188 
      • R-Value Observed: 0.188 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 37.385α = 90
      b = 38.683β = 109.18
      c = 30.072γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data scaling
      REFMACrefinement

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Howard Hughes Medical Institute (HHMI)United States--

      Revision History  (Full details and data files)

      • Version 1.0: 2014-08-13
        Type: Initial release
      • Version 1.1: 2014-09-17
        Changes: Database references
      • Version 1.2: 2014-10-01
        Changes: Database references
      • Version 1.3: 2014-10-15
        Changes: Database references
      • Version 1.4: 2015-01-14
        Changes: Database references
      • Version 1.5: 2015-08-26
        Changes: Data collection
      • Version 1.6: 2017-09-27
        Changes: Derived calculations, Refinement description
      • Version 1.7: 2019-11-20
        Changes: Author supporting evidence