5NXT

Wobble base paired RNA double helix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.379 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel form of RNA double helix based on G·U and C·A+ wobble base pairing.

Garg, A.Heinemann, U.

(2018) RNA 24: 209-218

  • DOI: 10.1261/rna.064048.117

  • PubMed Abstract: 
  • Wobble base pairs are critical in various physiological functions and have been linked to local structural perturbations in double helical structures of nucleic acids. We report a 1.38-Å resolution crystal structure of an antiparallel octadecamer RNA ...

    Wobble base pairs are critical in various physiological functions and have been linked to local structural perturbations in double helical structures of nucleic acids. We report a 1.38-Å resolution crystal structure of an antiparallel octadecamer RNA double helix in overall A conformation, which includes a unique, central stretch of six consecutive wobble base pairs (W helix) with two G·U and four rare C·A+ wobble pairs. Four adenines within the W helix are N1-protonated and wobble-base-paired with the opposing cytosine through two regular hydrogen bonds. Combined with the two G·U pairs, the C·A+ base pairs facilitate formation of a half turn of W-helical RNA flanked by six regular Watson-Crick base pairs in standard A conformation on either side. RNA melting experiments monitored by differential scanning calorimetry, UV and circular dichroism spectroscopy demonstrate that the RNA octadecamer undergoes a pH-induced structural transition which is consistent with the presence of a duplex with C·A+ base pairs at acidic pH. Our crystal structure provides a first glimpse of an RNA double helix based entirely on wobble base pairs with possible applications in RNA or DNA nanotechnology and pH biosensors.


    Organizational Affiliation

    Max Delbrück Center for Molecular Medicine.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*UP*UP*CP*UP*CP*UP*AP*CP*GP*AP*AP*GP*AP*AP*CP*A)-3')U18synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.379 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.130 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 44.997α = 90.00
b = 44.997β = 90.00
c = 94.205γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Germany--

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references, Derived calculations
  • Version 1.2: 2018-01-24
    Type: Database references