4U35

Crystal Structures of RNA Duplexes Containing 2-thio-Uridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

Starting Model: experimental
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This is version 1.8 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: https://doi.org/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. 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

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*AP*GP*CP*(SUR)P*CP*C-3')7synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*UP*GP*CP*UP*A)-3')7synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 21.681α = 90
b = 35.158β = 90
c = 47.304γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement

Structure Validation

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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
  • Version 1.8: 2023-09-27
    Changes: Data collection, Database references, Refinement description