6PMO

Co-crystal structure of the Geobacillus kaustophilus glyQ T-box riboswitch discriminator domain in complex with tRNA-Gly

  • Classification: RNA
  • Organism(s): Geobacillus kaustophilus

  • Deposited: 2019-07-02 Released: 2019-11-20 
  • Deposition Author(s): Li, S., Zhang, J.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65703 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions.

Li, S.Su, Z.Lehmann, J.Stamatopoulou, V.Giarimoglou, N.Henderson, F.E.Fan, L.Pintilie, G.D.Zhang, K.Chen, M.Ludtke, S.J.Wang, Y.X.Stathopoulos, C.Chiu, W.Zhang, J.

(2019) Nat.Struct.Mol.Biol. --: --

  • DOI: 10.1038/s41594-019-0326-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasi ...

    Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box-tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate 'discriminator' structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.


    Organizational Affiliation

    Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA.,Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Campus Paris-Saclay, Gif-sur-Yvette, France.,Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA.,Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.,Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, Stanford University, Stanford, CA, USA. wahc@stanford.edu.,Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA. jinwei.zhang@nih.gov.,Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA. wahc@stanford.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
tRNA-GlyB75Geobacillus kaustophilus
Entity ID: 2
MoleculeChainsLengthOrganism
T-box riboswitch discriminatorA66Geobacillus kaustophilus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IR
Query on IR

Download SDF File 
Download CCD File 
A, B
IRIDIUM ION
Ir
MOHYGSBMXIJZBJ-UHFFFAOYSA-N
 Ligand Interaction
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: 2.65703 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 44.851α = 90.00
b = 139.913β = 90.00
c = 136.023γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-07-02 
  • Released Date: 2019-11-20 
  • Deposition Author(s): Li, S., Zhang, J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesZIA-DK075136

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-04
    Type: Database references