4KZD

Crystal structure of an RNA aptamer in complex with fluorophore and Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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This is version 2.1 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
BL3-6 Fab antibody, heavy chainA [auth H]232Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BL3-6 Fab antibody, light chainB [auth L]215Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (84-MER)C [auth R]84N/A
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseD [auth A]2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.425α = 90
b = 79.602β = 111.65
c = 95.21γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
RAPDmodel building
PHENIXrefinement
HKL-2000data reduction
RAPDdata scaling
RAPDphasing

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: 2015-05-20
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary