7EAG

Crystal structure of the RAGATH-18 k-turn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules.

Huang, L.Liao, X.Li, M.Wang, J.Peng, X.Wilson, T.J.Lilley, D.M.J.

(2021) Nucleic Acids Res 49: 5916-5924

  • DOI: https://doi.org/10.1093/nar/gkab333
  • Primary Citation of Related Structures:  
    7EAF, 7EAG

  • PubMed Abstract: 

    k-Turns are widespread key architectural elements that occur in many classes of RNA molecules. We have shown previously that their folding properties (whether or not they fold into their tightly kinked structure on addition of metal ions) and conformation depend on their local sequence, and we have elucidated a series of rules for prediction of these properties from sequence. In this work, we have expanded the rules for prediction of folding properties, and then applied the full set to predict the folding and conformation of four probable k-turns we have identified amongst 224 structured RNA species found in bacterial intergenenic regions by the Breaker lab (1). We have analyzed the ion-dependence of folding of the four k-turns using fluorescence resonance energy transfer, and determined the conformation of two of them using X-ray crystallography. We find that the experimental data fully conform to both the predicted folding and conformational properties. We conclude that our folding rules are robust, and can be applied to new k-turns of unknown characteristics with confidence.


  • Organizational Affiliation

    Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, PR China.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*UP*CP*UP*AP*UP*GP*AP*AP*GP*GP*CP*UP*GP*GP*AP*GP*AP*C)-3')19Clostridium perfringens SM101
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.769α = 90
b = 74.908β = 90
c = 136.595γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, China)China--
Cancer Research UKUnited KingdomA18604

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description