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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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

    1] Department of Chemistry, University of Chicago, Chicago, Illinois, USA. [2] Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BL3-6 Fab antibody, heavy chain
H
232Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BL3-6 Fab antibody, light chain
L
215Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
RNA (84-MER)R84N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download CCD File 
H
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
1TU
Query on 1TU

Download CCD File 
R
4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol
C12 H12 F2 N2 O2
MSZRPLCUVKFQJC-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
R
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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