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 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1038/nchembio.1561
  • Primary Citation of Related Structures:  
    4KZD, 4KZE, 4Q9Q, 4Q9R

  • 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-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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab BL3-6, HEAVY CHAINA [auth H]223Mus musculusMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab BL3-6, LIGHT CHAINB [auth L]214Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
Spinach RNA aptamerC [auth R]84synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2ZY
Query on 2ZY

Download Ideal Coordinates CCD File 
E [auth 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
K
Query on K

Download Ideal Coordinates CCD File 
D [auth R]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.515α = 90
b = 78.986β = 112.42
c = 94.357γ = 90
Software Package:
Software NamePurpose
RAPDdata collection
PHENIXmodel building
PHENIXrefinement
RAPDdata reduction
RAPDdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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