4MGM

Crystal structure of the in vitro transcribed G. kaustophilus tRNA-Gly

  • Classification: RNA

  • Deposited: 2013-08-28 Released: 2013-10-23 
  • Deposition Author(s): Grigg, J.C., Ke, A.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Determinants for Geometry and Information Decoding of tRNA by T Box Leader RNA.

Grigg, J.C.Ke, A.

(2013) Structure 21: 2025-2032

  • DOI: 10.1016/j.str.2013.09.001
  • Primary Citation of Related Structures:  4MGN

  • PubMed Abstract: 
  • T box riboswitches are cis-acting RNA elements that bind to tRNA and sense its aminoacylation state to influence gene expression. Here, we present the 3.2 Å resolution X-ray crystal structures of the T box Stem I-tRNA complex and tRNA, in isolation. ...

    T box riboswitches are cis-acting RNA elements that bind to tRNA and sense its aminoacylation state to influence gene expression. Here, we present the 3.2 Å resolution X-ray crystal structures of the T box Stem I-tRNA complex and tRNA, in isolation. T box Stem I forms an arched conformation with extensive intermolecular contacts to two key points of tRNA, the anticodon and D/T-loops. Free and complexed tRNA exist in significantly different conformations, with the contacts stabilizing flexible D/T-loops and a rearrangement of the D-loop. Using a designed T box RNA/tRNA system, we demonstrate that the T box riboswitch monitors the length and orientation of two essential contacts. Length or orientation mismatches engineered into the T box riboswitch and tRNA disrupt the complex, whereas simultaneous insertion of full helical turns realigns the interfaces and restores interaction between artificially elongated T box riboswitch and tRNA molecules.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
tRNA glycineA,B75N/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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.248 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 161.233α = 90.00
b = 28.409β = 110.69
c = 132.939γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling
Adxvdata processing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-08-28 
  • Released Date: 2013-10-23 
  • Deposition Author(s): Grigg, J.C., Ke, A.

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description