8UTA

yjdF riboswitch from R. gauvreauii in complex with proflavine bound to Fab BL3-6 S97N

• PDB DOI: https://doi.org/10.2210/pdb8UTA/pdb
• NAKB: 8UTA

• Classification: RNA
• Organism(s): Ruminococcus gauvreauii, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-30 Released: 2024-04-10 
• Deposition Author(s): Krochmal, D., Lewicka, A., Piccirilli, J.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.269 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Literature

Structural basis for promiscuity in ligand recognition by yjdF riboswitch.

Krochmal, D., Roman, C., Lewicka, A., Shao, Y., Piccirilli, J.A.

(2024) Cell Discov 10: 37-37

• PubMed: 38565535 
• DOI: https://doi.org/10.1038/s41421-024-00663-2
• Primary Citation of Related Structures:  
  8UIW, 8UTA

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 179.17 kDa 
• Atom Count: 12,024 
• Modelled Residue Count: 1,131 
• Deposited Residue Count: 1,152 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab BL3-6 S97N heavy chain	C [auth A], D [auth H]	233	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab BL3-6 S97N light chain	E [auth B], F [auth L]	215	Mus musculus	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
yjdF RNA (R. gauvreauii)	A [auth N], B [auth R]	128	Ruminococcus gauvreauii

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRL (Subject of Investigation/LOI)	J [auth N], N [auth R]	PROFLAVIN C13 H11 N3 WDVSHHCDHLJJJR-UHFFFAOYSA-N
MG	G [auth N], H [auth N], I [auth N], K [auth R], L [auth R], M [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.269 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.873	α = 87.25
b = 75.138	β = 87.99
c = 95.727	γ = 87.72

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Krochmal, D., Lewicka, A., Piccirilli, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM149336

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Database references