5C7U

5'-monophosphate wt Guanine Riboswitch bound to hypoxanthine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair.

Hernandez, A.R.Shao, Y.Hoshika, S.Yang, Z.Shelke, S.A.Herrou, J.Kim, H.J.Kim, M.J.Piccirilli, J.A.Benner, S.A.

(2015) Angew Chem Int Ed Engl 54: 9853-9856

  • DOI: https://doi.org/10.1002/anie.201504731
  • Primary Citation of Related Structures:  
    5C7U, 5C7W

  • PubMed Abstract: 

    As one of its goals, synthetic biology seeks to increase the number of building blocks in nucleic acids. While efforts towards this goal are well advanced for DNA, they have hardly begun for RNA. Herein, we present a crystal structure for an RNA riboswitch where a stem C:G pair has been replaced by a pair between two components of an artificially expanded genetic-information system (AEGIS), Z and P, (6-amino-5-nitro-2(1H)-pyridone and 2-amino-imidazo[1,2-a]-1,3,5-triazin-4-(8H)-one). The structure shows that the Z:P pair does not greatly change the conformation of the RNA molecule nor the details of its interaction with a hypoxanthine ligand. This was confirmed in solution by in-line probing, which also measured a 3.7 nM affinity of the riboswitch for guanine. These data show that the Z:P pair mimics the natural Watson-Crick geometry in RNA in the first example of a crystal structure of an RNA molecule that contains an orthogonal added nucleobase pair.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA).


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
5'-monophosphate wt guanine riboswitchA [auth B]67Bacillus subtilis subsp. subtilis str. 168
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.6α = 90
b = 52.6β = 90
c = 278.12γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Defense Threat Reduction Agency (DTRA)United StatesHDTRA1-13-1-0004
National Aeronautic Space Administration (NASA, United States)United StatesNNX10AT28G
Templeton World Charitable FundUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description