Biological Assembly 1  

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Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39275.13 
• Atom Count: 2407 
• Residue Count: 112 
• Unique nucleic acid chains: 1

3F2W

Crystal structure of the FMn riboswitch bound to FMN, Ba2+ soak.

• DOI: 10.2210/pdb3F2W/pdb
• NDB: UR0173

• Classification: RNA


• Deposited: 2008-10-30 Released: 2009-01-27 
• Deposition Author(s): Serganov, A.A., Huang, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.217 
• R-Value Work: 0.181 

Literature

Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch.

Serganov, A., Huang, L., Patel, D.J.

(2009) Nature 458: 233-237

• PubMed: 19169240 
• DOI: 10.1038/nature07642
• Primary Citation of Related Structures:  
  3F4H, 3F4G, 3F4E, 3F30, 3F2Y, 3F2X, 3F2T, 3F2Q


• PubMed Abstract: 
  

The biosynthesis of several protein cofactors is subject to feedback regulation by riboswitches. Flavin mononucleotide (FMN)-specific riboswitches, also known as RFN elements, direct expression of bacterial genes involved in the biosynthesis and transport of riboflavin (vitamin B(2)) and related compounds. Here we present the crystal structures of the Fusobacterium nucleatum riboswitch bound to FMN, riboflavin and antibiotic roseoflavin. The FMN riboswitch structure, centred on an FMN-bound six-stem junction, does not fold by collinear stacking of adjacent helices, typical for folding of large RNAs. Rather, it adopts a butterfly-like scaffold, stapled together by opposingly directed but nearly identically folded peripheral domains. FMN is positioned asymmetrically within the junctional site and is specifically bound to RNA through interactions with the isoalloxazine ring chromophore and direct and Mg(2+)-mediated contacts with the phosphate moiety. Our structural data, complemented by binding and footprinting experiments, imply a largely pre-folded tertiary RNA architecture and FMN recognition mediated by conformational transitions within the junctional binding pocket. The inherent plasticity of the FMN-binding pocket and the availability of large openings make the riboswitch an attractive target for structure-based design of FMN-like antimicrobial compounds. Our studies also explain the effects of spontaneous and antibiotic-induced deregulatory mutations and provided molecular insights into FMN-based control of gene expression in normal and riboflavin-overproducing bacterial strains.

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Organizational Affiliation: 

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
FMN riboswitch	X	112	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FMN	X	FLAVIN MONONUCLEOTIDE RIBOFLAVIN MONOPHOSPHATE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
MG	X	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
BA	X	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CCC	X	RNA LINKING	C9 H13 N3 O10 P2		C
GTP	X	NON-POLYMER	C10 H16 N5 O14 P3		G

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.217 
• R-Value Work: 0.181 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 71.003	α = 90.00
b = 71.003	β = 90.00
c = 139.745	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-10-30 
• Released Date: 2009-01-27 
• Deposition Author(s): Serganov, A.A., Huang, L.

Revision History 

• Version 1.0: 2009-01-27
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Refinement description, Version format compliance