5NQI

E.coli 16S rRNA Sarcin-Ricin Loop containing a 5-hydroxymethylcytosine modification


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.851 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine.

Riml, C.Lusser, A.Ennifar, E.Micura, R.

(2017) J. Org. Chem. 82: 7939-7945

  • DOI: 10.1021/acs.joc.7b01171

  • PubMed Abstract: 
  • 5-Hydroxymethylcytosine (hm5C) is an RNA modification that has attracted significant interest because of the finding that RNA hydroxymethylation can favor mRNA translation. For insight into the mechanistic details of hm5C function to be obtained, the ...

    5-Hydroxymethylcytosine (hm5C) is an RNA modification that has attracted significant interest because of the finding that RNA hydroxymethylation can favor mRNA translation. For insight into the mechanistic details of hm5C function to be obtained, the availability of RNAs containing this modification at defined positions that can be used for in vitro studies is highly desirable. In this work, we present an eight-step route to 5-hydroxymethylcytidine (hm5rC) phosphoramidite for solid-phase synthesis of modified RNA oligonucleotides. Furthermore, we examined the effects of hm5rC on RNA duplex stability and its impact on structure formation using the sarcin-ricin loop (SRL) motif. Thermal denaturation experiments revealed that hm5rC increases RNA duplex stability. By contrast, when cytosine within an UNCG tetraloop motif was replaced by hm5rC, the thermodynamic stability of the corresponding hairpin fold was attenuated. Importantly, incorporation of hm5rC into the SRL motif resulted in an RNA crystal structure at 0.85 Å resolution. Besides changes in the hydration pattern at the site of modification, a slight opening of the hm5rC-G pair compared to the unmodified C-G in the native structure was revealed.


    Organizational Affiliation

    Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck , 6020 Innsbruck, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
E.Coli 27-mer SRL RNAA27Escherichia coli
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5HM
Query on 5HM
A
RNA LINKINGC10 H16 N3 O9 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.851 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.146 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 29.510α = 90.00
b = 29.510β = 90.00
c = 76.800γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-16
    Type: Database references