4Q9R

Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.

Huang, H.Suslov, N.B.Li, N.S.Shelke, S.A.Evans, M.E.Koldobskaya, Y.Rice, P.A.Piccirilli, J.A.

(2014) Nat.Chem.Biol. 10: 686-691

  • DOI: 10.1038/nchembio.1561
  • Primary Citation of Related Structures:  4KZD, 4KZE, 4Q9Q

  • PubMed Abstract: 
  • Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assiste ...

    Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.


    Organizational Affiliation

    Department of Chemistry, University of Chicago, Chicago, Illinois, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab BL3-6, HEAVY CHAIN
H
223N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab BL3-6, LIGHT CHAIN
L
214N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsLengthOrganism
Spinach RNA aptamerR84synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
R
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
2ZY
Query on 2ZY

Download SDF File 
Download CCD File 
R
(5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one
C13 H9 F5 N2 O2
AWYCLBWNRONMQC-WMZJFQQLSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GDP
Query on GDP
R
RNA LINKINGC10 H15 N5 O11 P2G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 147.515α = 90.00
b = 78.986β = 112.42
c = 94.357γ = 90.00
Software Package:
Software NamePurpose
RAPDdata scaling
PHENIXmodel building
RAPDdata collection
RAPDdata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-09
    Type: Database references
  • Version 1.2: 2014-07-30
    Type: Database references
  • Version 1.3: 2014-10-15
    Type: Structure summary
  • Version 2.0: 2017-07-26
    Type: Advisory, Atomic model, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary