6V9D

Co-crystal structure of the fluorogenic Mango-IV homodimer bound to TO1-Biotin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report



Literature

Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair.

Trachman 3rd, R.J.Cojocaru, R.Wu, D.Piszczek, G.Ryckelynck, M.Unrau, P.J.Ferre-D'Amare, A.R.

(2020) Structure 

  • DOI: 10.1016/j.str.2020.04.007
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Fluorescent RNA aptamers have been used in cells as biosensor reporters and tags for tracking transcripts. Recently, combined SELEX and microfluidic fluorescence sorting yielded three aptamers that activate fluorescence of TO1-Biotin: Mango-II, Mango ...

    Fluorescent RNA aptamers have been used in cells as biosensor reporters and tags for tracking transcripts. Recently, combined SELEX and microfluidic fluorescence sorting yielded three aptamers that activate fluorescence of TO1-Biotin: Mango-II, Mango-III, and Mango-IV. Of these, Mango-IV was best at imaging RNAs in both fixed and live mammalian cells. To understand how Mango-IV achieves activity in cells, we determined its crystal structure complexed with TO1-Biotin. The structure reveals a domain-swapped homodimer with two independent G-quadruplex fluorophore binding pockets. Structure-based analyses indicate that the Mango-IV core has relaxed fluorophore specificity, and a tendency to reorganize binding pocket residues. These molecular properties may endow it with robustness in the cellular milieu. Based on the domain-swapped structure, heterodimers between Mango-IV and the fluorescent aptamer iSpinach, joined by Watson-Crick base pairing, were constructed. These exhibited FRET between their respective aptamer-activated fluorophores, advancing fluorescent aptamer technology toward multi-color, RNA-based imaging of RNA coexpression and colocalization.


    Organizational Affiliation

    Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA. Electronic address: adrian.ferre@nih.gov.



Macromolecules

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (28-MER)B, E28synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QW4
Query on QW4

Download CCD File 
B, E
2-[(E)-(1-methylquinolin-4(1H)-ylidene)methyl]-3-(2-oxopropyl)-1,3-benzothiazol-3-ium
C21 H19 N2 O S
MNJLWFGXGDINRC-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download CCD File 
B, E
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
K
Query on K

Download CCD File 
B, E
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.225 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.917α = 90
b = 48.917β = 90
c = 122.972γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-05-20
    Type: Initial release