3IIN

Plasticity of the kink turn structural motif

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.18 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.292 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Plasticity of the RNA kink turn structural motif.

Antonioli, A.H., Cochrane, J.C., Lipchock, S.V., Strobel, S.A.

(2010) RNA 16: 762-768

  • DOI: 10.1261/rna.1883810
  • Primary Citation of Related Structures:  
    3IIN

  • PubMed Abstract: 

    • The kink turn (K-turn) is an RNA structural motif found in many biologically significant RNAs. While most examples of the K-turn have a similar fold, the crystal structure of the Azoarcus group I intron revealed a novel RNA conformation, a reverse kink turn bent in the direction opposite that of a consensus K-turn ...

    The kink turn (K-turn) is an RNA structural motif found in many biologically significant RNAs. While most examples of the K-turn have a similar fold, the crystal structure of the Azoarcus group I intron revealed a novel RNA conformation, a reverse kink turn bent in the direction opposite that of a consensus K-turn. The reverse K-turn is bent toward the major grooves rather than the minor grooves of the flanking helices, yet the sequence differs from the K-turn consensus by only a single nucleotide. Here we demonstrate that the reverse bend direction is not solely defined by internal sequence elements, but is instead affected by structural elements external to the K-turn. It bends toward the major groove under the direction of a tetraloop-tetraloop receptor. The ability of one sequence to form two distinct structures demonstrates the inherent plasticity of the K-turn sequence. Such plasticity suggests that the K-turn is not a primary element in RNA folding, but instead is shaped by other structural elements within the RNA or ribonucleoprotein assembly.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein A A95Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
NIH Common Fund Data Resources
PHAROS:  P09012
GTEx:  ENSG00000077312
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
Group I intronB197N/A
Find similar nucleic acids by: Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA/RNA (5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*GP*AP*CP*C)-D(P*AP*GP*A)-R(P*CP*GP*GP*CP*C)-3')C22N/A
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    DNA/RNA (5'-R(*CP*A)-D(P*T)-3')D3N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 4.18 Å
    • R-Value Free: 0.323 
    • R-Value Work: 0.290 
    • R-Value Observed: 0.292 
    • Space Group: P 41 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 109.826α = 90
    b = 109.826β = 90
    c = 250.218γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    REFMACrefinement
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2010-03-09
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2017-11-01
      Changes: Refinement description