9J4O | pdb_00009j4o

Crystal structure of B. subtilis Leucine tRNA with UAA anticodon

• PDB DOI: https://doi.org/10.2210/pdb9J4O/pdb
• NAKB: 9J4O

• Classification: RNA
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2024-08-09 Released: 2025-07-09 
• Deposition Author(s): Kim, J., Cho, G.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.263 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: in silico

Literature

Crystal structures of free-state tRNA Leu reveal conformational flexibility of type-II tRNAs.

Cho, G., Yoo, J., Shin, K., Lee, J., Lim, J., Kim, J.

(2025) RNA 31: 1305-1319

• PubMed: 40562537 
• DOI: https://doi.org/10.1261/rna.080596.125
• Primary Citation Related Structures: 
  9J4N, 9J4O


• PubMed Abstract: 
  

  Transfer RNAs (tRNAs) are classified into Type-I and Type-II based on the length of their variable loops, with Type-II characterized by an extended variable loop. While structures of Type-I tRNAs have been well-documented, standalone structures of Type-II tRNAs have not been reported. Here, we present the first crystal structures of two free-state Type-II tRNAs, specifically tRNALeu from Bacillus subtilis and Escherichia coli. Our structures reveal that the B. subtilis tRNALeu anticodon stem-loop (ASL) retains its canonical conformation. The variable loops in both structures are well-defined, displaying a distinctive tetranucleotide loop conformation. Comparisons with Type-I tRNA and biomolecule-bound tRNAs highlight the flexibility of the ASL, variable loop, and terminal CCA residues in Type-II tRNAs, suggesting that this structural plasticity is crucial for their biological interactions and function. These findings provide new insights into the structural dynamics and functional roles of Type-II tRNAs.

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Organizational Affiliation: 
• 65419 Gwangju Institute of Science and Technology Gwangju Institute of Science and Technology.
65419 Gwangju Institute of Science and Technology Gwangju Institute of Science and Technology [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.95 kDa 
• Atom Count: 1,880 
• Modeled Residue Count: 87 
• Deposited Residue Count: 89 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Leucine tRNA_UAA (89-MER)	A	89	Bacillus subtilis subsp. subtilis str. 168

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	B [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.263 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.19	α = 90
b = 37.2	β = 99.45
c = 81.99	γ = 90

Software Package:

Software Name	Purpose
MxDC	data collection
autoPROC	data processing
autoPROC	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Kim, J., Cho, G.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release
  
• Version 1.1: 2025-09-03
  Changes: Database references