Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 36154.26 
• Atom Count: 2373 
• Residue Count: 110 
• Unique nucleic acid chains: 2

6DN3

CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1555 SPLIT RNA

• DOI: 10.2210/pdb6DN3/pdb

• Classification: RNA
• Organism(s): Fusobacterium nucleatum


• Deposited: 2018-06-05 Released: 2018-09-05 
• Deposition Author(s): Vicens, Q., Mondragon, E., Reyes, F.E., Berman, J., Kaur, H., Kells, K., Wickens, P., Wilson, J., Gadwood, R., Schostarez, H., Suto, R.K., Coish, P., Blount, K.F., Batey, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.229 
• R-Value Work: 0.193 

Literature

Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch.

Vicens, Q., Mondragon, E., Reyes, F.E., Coish, P., Aristoff, P., Berman, J., Kaur, H., Kells, K.W., Wickens, P., Wilson, J., Gadwood, R.C., Schostarez, H.J., Suto, R.K., Blount, K.F., Batey, R.T.

(2018) ACS Chem. Biol. 13: 2908-2919

• PubMed: 30107111 
• DOI: 10.1021/acschembio.8b00533
• Primary Citation of Related Structures:  
  6DN2, 6DN1


• PubMed Abstract: 
  

The flavin mononucleotide (FMN) riboswitch is an emerging target for the development of novel RNA-targeting antibiotics. We previously discovered an FMN derivative -5FDQD- that protects mice against diarrhea-causing Clostridium difficile bacteria. Here, we present the structure-based drug design strategy that led to the discovery of this fluoro-phenyl derivative with antibacterial properties. This approach involved the following stages: (1) structural analysis of all available free and bound FMN riboswitch structures; (2) design, synthesis and purification of derivatives; (3) in vitro testing for productive binding using two chemical probing methods; (4) in vitro transcription termination assays; (5) resolution of the crystal structures of the FMN riboswitch in complex with the most mature candidates. In the process, we delineated principles for productive binding to this riboswitch, thereby demonstrating the effectiveness of a coordinated structure-guided approach to designing drugs against RNA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
RNA RIBOSWITCH	X	54	Fusobacterium nucleatum

Entity ID: 2
Molecule	Chains	Length	Organism
RNA (56-MER)	Y	56	Fusobacterium nucleatum

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	Y	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	X	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	X, Y	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
GZ4	Y	7,8-dimethyl-2,4-dioxo-10-(3-phenylpropyl)-1,2,3,4-tetrahydrobenzo[g]pteridin-10-ium C21 H21 N4 O2 LVUMBLZQGDFTPC-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.229 
• R-Value Work: 0.193 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 71.550	α = 90.00
b = 71.550	β = 90.00
c = 140.270	γ = 120.00

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-06-05 
• Released Date: 2018-09-05 
• Deposition Author(s): Vicens, Q., Mondragon, E., Reyes, F.E., Berman, J., Kaur, H., Kells, K., Wickens, P., Wilson, J., Gadwood, R., Schostarez, H., Suto, R.K., Coish, P., Blount, K.F., Batey, R.T.

Revision History 

• Version 1.0: 2018-09-05
  Type: Initial release
• Version 1.1: 2018-10-03
  Type: Data collection, Database references
• Version 1.2: 2018-10-31
  Type: Data collection, Database references