6CU1

X-ray structure of the S. typhimurium YrlA effector-binding module

• PDB DOI: https://doi.org/10.2210/pdb6CU1/pdb
• NAKB: 6CU1

• Classification: RNA
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Mutation(s): No 


• Deposited: 2018-03-23 Released: 2018-10-31 
• Deposition Author(s): Wang, W., Chen, X., Wolin, S.L., Xiong, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Literature

Structural Basis for tRNA Mimicry by a Bacterial Y RNA.

Wang, W., Chen, X., Wolin, S.L., Xiong, Y.

(2018) Structure 26: 1635

• PubMed: 30318468 
• DOI: https://doi.org/10.1016/j.str.2018.09.001
• Primary Citation of Related Structures:  
  6CU1


• PubMed Abstract: 
  

  Noncoding Y RNAs are present in both animal cells and many bacteria. In all species examined, Y RNAs tether the Ro60 protein to an effector protein to perform various cellular functions. Recently, a new Y RNA subfamily was identified in bacteria. Bioinformatic analyses of these YrlA (Y RNA-like A) RNAs predict that the effector-binding domain resembles tRNA. We present the structure of this domain, the overall folding of which is strikingly similar to canonical tRNAs. The tertiary interactions that are responsible for stabilizing tRNA are present in YrlA, making it a close tRNA mimic. However, YrlA lacks a free CCA end and contains a kink in the stem corresponding to the anticodon stem. Since nucleotides in the D and T stems are conserved among YrlAs, they may be an interaction site for an unknown factor. Our experiments identify YrlA RNAs as a new class of tRNA mimics.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.44 kDa 
• Atom Count: 1,736 
• Modelled Residue Count: 80 
• Deposited Residue Count: 81 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
YrlA effector-binding module	A	81	Salmonella enterica subsp. enterica serovar Typhimurium

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.409	α = 90
b = 147.108	β = 90
c = 101.564	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Wang, W., Chen, X., Wolin, S.L., Xiong, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM073863
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI116313

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations