5G4V

Association of four two-k-turn units based on Kt-7 3bG,3nC, forming a square-shaped structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

A Quasi-Cyclic RNA Nano-Scale Molecular Object Constructed Using Kink Turns.

Huang, L.Lilley, D.M.J.

(2016) Nanoscale 8: 15189

  • DOI: https://doi.org/10.1039/c6nr05186c
  • Primary Citation of Related Structures:  
    5G4T, 5G4U, 5G4V

  • PubMed Abstract: 

    k-Turns are widespread RNA architectural elements that mediate tertiary interactions. We describe a double-kink-turn motif comprising two inverted k-turns that forms a tight horse-shoe structure that can assemble into a variety of shapes by coaxial association of helical ends. Using X-ray crystallography we show that these assemble with two (dumbell), three (triangle) and four units (square), with or without bound protein, within the crystal lattice. In addition, exchange of a single basepair can almost double the pore radius or shape of a molecular assembly. On the basis of this analysis we synthesized a 114 nt self-complementary RNA containing six k-turns. The crystal structure of this species shows that it forms a quasi-cyclic triangular object. These are randomly disposed about the three-fold axis in the crystal lattice, generating a circular RNA of quasi D3 symmetry with a shape reminiscent of that of a cyclohexane molecule in its chair conformation. This work demonstrates that the k-turn is a powerful building block in the construction of nano-scale molecular objects, and illustrates why k-turns are widely used in natural RNA molecules to organize long-range architecture and mediate tertiary contacts.


  • Organizational Affiliation

    Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK. d.m.j.lilley@dundee.ac.uk l.y.huang@dundee.ac.uk.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L7AE
C, D, G, H
123Archaeoglobus fulgidusMutation(s): 0 
UniProt
Find proteins for O29494 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29494 
Go to UniProtKB:  O29494
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29494
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
HMKT-7
A, B, E, F
19Haloarcula marismortui
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.65α = 90
b = 70.64β = 105.48
c = 92.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description