6POM | pdb_00006pom

Cryo-EM structure of the full-length Bacillus subtilis glyQS T-box riboswitch in complex with tRNA-Gly

• PDB DOI: https://doi.org/10.2210/pdb6POM/pdb
• NAKB: 6POM
• EM Map EMD-20416: EMDB EMDataResource

• Classification: RNA
• Organism(s): Bacillus subtilis
• Expression System: in vitro transcription vector pT7-TP(deltai)
• Mutation(s): No 


• Deposited: 2019-07-04 Released: 2019-11-20 
• Deposition Author(s): Li, S., Su, Z., Zhang, J., Chiu, W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

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 26: 1094-1105

• PubMed: 31740854 
• DOI: https://doi.org/10.1038/s41594-019-0326-7
• Primary Citation Related Structures: 
  6PMO, 6POM


• 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 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.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA.
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Campus Paris-Saclay, Gif-sur-Yvette, France.
Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece.
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.
Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA. [e-mail].
Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, Stanford University, Stanford, CA, USA. [e-mail].
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry, native gel electrophoresis, gel filtration

Macromolecule Content 

• Total Structure Weight: 78.89 kDa 
• Atom Count: 4,937 
• Modeled Residue Count: 230 
• Deposited Residue Count: 244 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
T-box GlyQS leader (155-MER)	A	169	Bacillus subtilis

Entity ID: 2
Molecule	Chains	Length	Organism	Image
tRNAGly (75-MER)	B	75	Bacillus subtilis

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0-beta
RECONSTRUCTION	cryoSPARC	2.2
MODEL REFINEMENT	PHENIX	1.15.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Li, S., Su, Z., Zhang, J., Chiu, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P50GM103297

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Database references
• Version 1.2: 2019-12-18
  Changes: Database references
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references, Refinement description