4NFP

Crystal Structure Analysis of the 16mer GCAGNCUUAAGUCUGC containing 8-aza-7-deaza-7-ethynyl Adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA.

Phelps, K.J.Ibarra-Soza, J.M.Tran, K.Fisher, A.J.Beal, P.A.

(2014) Acs Chem.Biol. 9: 1780-1787

  • DOI: 10.1021/cb500270x
  • Primary Citation of Related Structures:  4NFO, 4NFQ

  • PubMed Abstract: 
  • Ribonucleoside analogues bearing terminal alkynes, including 7-ethynyl-8-aza-7-deazaadenosine (7-EAA), are useful for RNA modification applications. However, although alkyne- and triazole-bearing ribonucleosides are in widespread use, very little inf ...

    Ribonucleoside analogues bearing terminal alkynes, including 7-ethynyl-8-aza-7-deazaadenosine (7-EAA), are useful for RNA modification applications. However, although alkyne- and triazole-bearing ribonucleosides are in widespread use, very little information is available on the impact of these modifications on RNA structure. By solving crystal structures for RNA duplexes containing these analogues, we show that, like adenosine, 7-EAA and a triazole derived from 7-EAA base pair with uridine and are well-accommodated within an A-form helix. We show that copper-catalyzed azide/alkyne cycloaddition (CuAAC) reactions with 7-EAA are sensitive to the RNA secondary structure context, with single-stranded sites reacting faster than duplex sites. 7-EAA and its triazole products are recognized in RNA template strands as adenosine by avian myoblastosis virus reverse transcriptase. In addition, 7-EAA in RNA is a substrate for an active site mutant of the RNA editing adenosine deaminase, ADAR2. These studies extend our understanding of the impact of these novel nucleobase analogues and set the stage for their use in probing RNA structure and metabolism.


    Organizational Affiliation

    Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
GCAG(A7E)CUUAAGUCUGCA,B,C16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARF
Query on ARF

Download SDF File 
Download CCD File 
A, B, C
FORMAMIDE
C H3 N O
ZHNUHDYFZUAESO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
A7E
Query on A7E
A, B, C
RNA LINKINGC12 H14 N5 O7 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.800α = 90.00
b = 43.190β = 120.82
c = 48.790γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-09-03
    Type: Database references