7E9E | pdb_00007e9e

Crystal structure of a class I PreQ1 riboswitch aptamer (ab13-14) complexed with a cognate ligand-derived photoaffinity probe

• PDB DOI: https://doi.org/10.2210/pdb7E9E/pdb
• NAKB: 7E9E

• Classification: RNA
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis
• Mutation(s): No 


• Deposited: 2021-03-04 Released: 2021-11-17 
• Deposition Author(s): Numata, T., Schneekloth, J.S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.208 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

A chemical probe based on the PreQ 1 metabolite enables transcriptome-wide mapping of binding sites.

Balaratnam, S., Rhodes, C., Bume, D.D., Connelly, C., Lai, C.C., Kelley, J.A., Yazdani, K., Homan, P.J., Incarnato, D., Numata, T., Schneekloth Jr., J.S.

(2021) Nat Commun 12: 5856-5856

• PubMed: 34615874 
• DOI: https://doi.org/10.1038/s41467-021-25973-x
• Primary Citation Related Structures: 
  7E9E, 7E9I


• PubMed Abstract: 
  

  The role of metabolite-responsive riboswitches in regulating gene expression in bacteria is well known and makes them useful systems for the study of RNA-small molecule interactions. Here, we study the PreQ ₁ riboswitch system, assessing sixteen diverse PreQ ₁ -derived probes for their ability to selectively modify the class-I PreQ ₁ riboswitch aptamer covalently. For the most active probe (11), a diazirine-based photocrosslinking analog of PreQ ₁ , X-ray crystallography and gel-based competition assays demonstrated the mode of binding of the ligand to the aptamer, and functional assays demonstrated that the probe retains activity against the full riboswitch. Transcriptome-wide mapping using Chem-CLIP revealed a highly selective interaction between the bacterial aptamer and the probe. In addition, a small number of RNA targets in endogenous human transcripts were found to bind specifically to 11, providing evidence for candidate PreQ ₁ aptamers in human RNA. This work demonstrates a stark influence of linker chemistry and structure on the ability of molecules to crosslink RNA, reveals that the PreQ ₁ aptamer/ligand pair are broadly useful for chemical biology applications, and provides insights into how PreQ ₁ , which is similar in structure to guanine, interacts with human RNAs.

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Organizational Affiliation: 
• Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
Center for Cancer Research Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.
Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-shi, Fukuoka, 812-8582, Japan.
Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki, 305-8566, Japan.
Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 10.9 kDa 
• Atom Count: 815 
• Modeled Residue Count: 33 
• Deposited Residue Count: 33 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
33-mer RNA	A	33	Caldanaerobacter subterraneus subsp. tengcongensis

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J0C	B [auth A]	2-azanyl-5-[[2-(3-but-3-ynyl-1,2-diazirin-3-yl)ethylamino]methyl]-1,7-dihydropyrrolo[2,3-d]pyrimidin-4-one C14 H17 N7 O XAJHFEIBEFHTRZ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.208 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.691	α = 90
b = 52.691	β = 90
c = 176.999	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Numata, T., Schneekloth, J.S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20K21281
Japan Society for the Promotion of Science (JSPS)	Japan	16KK0166

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description