Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.90 kDa 
• Atom Count: 2102 
• Modelled Residue Count: 94 
• Deposited Residue Count: 94 
• Unique nucleic acid chains: 1

3IQN

Free-state structural transitions of the SAM-I riboswitch

• PDB DOI: 10.2210/pdb3IQN/pdb

• Classification: RNA
• Mutation(s): No 


• Deposited: 2009-08-20 Released: 2010-08-04 
• Deposition Author(s): Montange, R.K., Batey, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.299 
• R-Value Work: 0.259 
• R-Value Observed: 0.259 

Literature

Free state conformational sampling of the SAM-I riboswitch aptamer domain.

Stoddard, C.D., Montange, R.K., Hennelly, S.P., Rambo, R.P., Sanbonmatsu, K.Y., Batey, R.T.

(2010) Structure 18: 787-797

• PubMed: 20637415 
• DOI: 10.1016/j.str.2010.04.006
• Primary Citation of Related Structures:  
  3IQN, 3IQP, 3IQR


• PubMed Abstract: 
  

Riboswitches are highly structured elements residing in the 5' untranslated region of messenger RNAs that specifically bind cellular metabolites to alter gene expression. While there are many structures of ligand-bound riboswitches that reveal details of bimolecular recognition, their unliganded structures remain poorly characterized. Characterizing the molecular details of the unliganded state is crucial for understanding the riboswitch's mechanism of action because it is this state that actively interrogates the cellular environment and helps direct the regulatory outcome. To develop a detailed description of the ligand-free form of an S-adenosylmethionine binding riboswitch at the local and global levels, we have employed a series of biochemical, biophysical, and computational methods. Our data reveal that the ligand binding domain adopts an ensemble of states that minimizes the energy barrier between the free and bound states to establish an efficient decision making branchpoint in the regulatory process.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, CO 80309-0215, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
SAM-I riboswitch	A	94	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	L [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
BA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
K	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.299 
• R-Value Work: 0.259 
• R-Value Observed: 0.259 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.98	α = 90
b = 61.98	β = 90
c = 159.07	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-20 
• Released Date: 2010-08-04 
Deposition Author(s): Montange, R.K., Batey, R.T.

Revision History  

• Version 1.0: 2010-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-04-04
  Changes: Data collection