5NS4

Crystal structures of Cy3 cyanine fluorophores stacked onto the end of double-stranded RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


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Literature

Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA.

Liu, Y.Lilley, D.M.J.

(2017) Biophys. J. 113: 2336-2343

  • DOI: 10.1016/j.bpj.2017.10.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The indodicarbocyanine fluorophores Cy3 and Cy5 are extensively used as donor-acceptor pairs in fluorescence resonance energy transfer experiments, especially those involving single molecules. When terminally attached to double-stranded nucleic acids ...

    The indodicarbocyanine fluorophores Cy3 and Cy5 are extensively used as donor-acceptor pairs in fluorescence resonance energy transfer experiments, especially those involving single molecules. When terminally attached to double-stranded nucleic acids via the 5' phosphate group these fluorophores stack onto the ends of the molecule. Knowledge of the positions of the fluorophores is critical to the interpretation of fluorescence resonance energy transfer data. The positions have been demonstrated for double-stranded (ds) DNA using NMR spectroscopy. Here, we have used x-ray crystallography to analyze the location of Cy3 and Cy5 on dsRNA, using complexes of an RNA stem-loop bound to L5 protein determined at 2.4 Å resolution. This confirms the tendency of both fluorophores to stack on the free end of RNA, with the long axis of the fluorophores approximately parallel to that of the terminal basepair. However, the manner of interaction of both Cy3 and Cy5 with the terminus of the dsRNA is significantly different from that deduced for dsDNA using NMR. The fluorophores are stacked on the terminal basepair such that their indole nitrogen atoms lie on the major groove side, and thus their pendant methyl groups are on the minor groove side.


    Organizational Affiliation

    Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
A, B
178Thermus thermophilusMutation(s): 0 
Gene Names: rplE (rpl5)
Find proteins for P41201 (Thermus thermophilus)
Go to UniProtKB:  P41201
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (34-MER)C,D33Thermus thermophilus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
96T
Query on 96T

Download SDF File 
Download CCD File 
C
3-[(2~{Z})-2-[(~{E})-3-[3,3-dimethyl-1-(3-oxidanylpropyl)indol-1-ium-2-yl]prop-2-enylidene]-3,3-dimethyl-indol-1-yl]propan-1-ol
C29 H37 N2 O2
RABDLLNSNYDNIC-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.260 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.757α = 90.00
b = 122.432β = 90.00
c = 51.013γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHENIXphasing
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release