5V3F

Co-crystal structure of the fluorogenic RNA Mango


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for high-affinity fluorophore binding and activation by RNA Mango.

Trachman, R.J.Demeshkina, N.A.Lau, M.W.L.Panchapakesan, S.S.S.Jeng, S.C.Y.Unrau, P.J.Ferre-D'Amare, A.R.

(2017) Nat. Chem. Biol. 13: 807-813

  • DOI: 10.1038/nchembio.2392

  • PubMed Abstract: 
  • Genetically encoded fluorescent protein tags have revolutionized proteome studies, whereas the lack of intrinsically fluorescent RNAs has hindered transcriptome exploration. Among several RNA-fluorophore complexes that potentially address this proble ...

    Genetically encoded fluorescent protein tags have revolutionized proteome studies, whereas the lack of intrinsically fluorescent RNAs has hindered transcriptome exploration. Among several RNA-fluorophore complexes that potentially address this problem, RNA Mango has an exceptionally high affinity for its thiazole orange (TO)-derived fluorophore, TO1-Biotin (Kd ∼3 nM), and, in complex with related ligands, it is one of the most redshifted fluorescent macromolecular tags known. To elucidate how this small aptamer exhibits such properties, which make it well suited for studying low-copy cellular RNAs, we determined its 1.7-Å-resolution co-crystal structure. Unexpectedly, the entire ligand, including TO, biotin and the linker connecting them, abuts one of the near-planar faces of the three-tiered G-quadruplex. The two heterocycles of TO are held in place by two loop adenines and form a 45° angle with respect to each other. Minimizing this angle would increase quantum yield and further improve this tool for in vivo RNA visualization.


    Organizational Affiliation

    Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (31-MER)A,B31synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
74G
Query on 74G

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Download CCD File 
A, B
4-{[(2S)-3-{2,16-dioxo-20-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-2,3-dihydro-1,3-benzothiazol-2-yl]methyl}-1-methylquinolin-1-ium
C38 H51 N6 O6 S2
BXBHTLUUPXOIJA-SDUHKGLLSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.199α = 90.00
b = 63.199β = 90.00
c = 138.413γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
SHELXCDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-14
    Type: Database references
  • Version 1.2: 2017-06-28
    Type: Database references