5KPY

Structure of a 5-hydroxytryptophan aptamer

  • Classification: RNA
  • Organism(s): unidentified
  • Mutation(s): No 

  • Deposited: 2016-07-05 Released: 2017-01-11 
  • Deposition Author(s): Batey, R.T., Porter, E., Merck, M.
  • Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors.

Porter, E.B.Polaski, J.T.Morck, M.M.Batey, R.T.

(2017) Nat Chem Biol 13: 295-301

  • DOI: 10.1038/nchembio.2278
  • Primary Citation of Related Structures:  
    5KPY

  • PubMed Abstract: 
  • Allosteric RNA devices are increasingly being viewed as important tools capable of monitoring enzyme evolution, optimizing engineered metabolic pathways, facilitating gene discovery and regulators of nucleic acid-based therapeutics. A key bottleneck in the development of these platforms is the availability of small-molecule-binding RNA aptamers that robustly function in the cellular environment ...

    Allosteric RNA devices are increasingly being viewed as important tools capable of monitoring enzyme evolution, optimizing engineered metabolic pathways, facilitating gene discovery and regulators of nucleic acid-based therapeutics. A key bottleneck in the development of these platforms is the availability of small-molecule-binding RNA aptamers that robustly function in the cellular environment. Although aptamers can be raised against nearly any desired target through in vitro selection, many cannot easily be integrated into devices or do not reliably function in a cellular context. Here, we describe a new approach using secondary- and tertiary-structural scaffolds derived from biologically active riboswitches and small ribozymes. When applied to the neurotransmitter precursors 5-hydroxytryptophan and 3,4-dihydroxyphenylalanine, this approach yielded easily identifiable and characterizable aptamers predisposed for coupling to readout domains to allow engineering of nucleic acid-sensory devices that function in vitro and in the cellular context.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado USA.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
5-hydroxytryptophan RNA aptamerA71unidentified
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IRI
Query on IRI

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , 
C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
4PQ (Subject of Investigation/LOI)
Query on 4PQ

Download Ideal Coordinates CCD File 
B [auth A]5-hydroxy-L-tryptophan
C11 H12 N2 O3
LDCYZAJDBXYCGN-VIFPVBQESA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.553α = 90
b = 26.594β = 106.32
c = 63.367γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystalCleardata reduction
d*TREKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1150834

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2017-03-01
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence