3MEI

Regulatory motif from the thymidylate synthase mRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.968 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA.

Dibrov, S.McLean, J.Hermann, T.

(2011) Acta Crystallogr.,Sect.D 67: 97-104

  • DOI: 10.1107/S0907444910050900

  • PubMed Abstract: 
  • A sequence around the start codon of the mRNA of human thymidylate synthase (TS) folds into a secondary-structure motif in which the initiation site is sequestered in a metastable hairpin. Binding of the protein to its own mRNA at the hairpin prevent ...

    A sequence around the start codon of the mRNA of human thymidylate synthase (TS) folds into a secondary-structure motif in which the initiation site is sequestered in a metastable hairpin. Binding of the protein to its own mRNA at the hairpin prevents the production of TS through a translation-repression feedback mechanism. Stabilization of the mRNA hairpin by other ligands has been proposed as a strategy to reduce TS levels in anticancer therapy. Rapidly proliferating cells require high TS activity to maintain the production of thymidine as a building block for DNA synthesis. The crystal structure of a model oligonucleotide (TS1) that represents the TS-binding site of the mRNA has been determined. While fluorescence studies showed that the TS1 RNA preferentially adopts a hairpin structure in solution, even at high RNA concentrations, an asymmetric dimer of two hybridized TS1 strands was obtained in the crystal. The TS1 dimer contains an unusual S-turn motif that also occurs in the `off' state of the human ribosomal decoding site RNA.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*GP*CP*CP*GP*CP*GP*CP*CP*AP*(5BU)P*GP*CP*CP*UP*GP*UP*GP*GP*CP*GP*G)-3')A,B23N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5BU
Query on 5BU
A, B
RNA LINKINGC9 H12 Br N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.968 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 32.928α = 90.00
b = 38.564β = 100.10
c = 41.985γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
MAR345dtbdata collection
CNSrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description
  • Version 1.4: 2019-07-17
    Type: Data collection, Derived calculations, Refinement description