Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.64 kDa 
• Atom Count: 1711 
• Modelled Residue Count: 79 
• Deposited Residue Count: 83 
• Unique nucleic acid chains: 1

2HOL

Crystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, barium ions

• PDB DOI: 10.2210/pdb2HOL/pdb

• Classification: RNA
• Mutation(s): No 


• Deposited: 2006-07-14 Released: 2006-09-19 
• Deposition Author(s): Edwards, T.E., Ferre-D'Amare, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.244 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition

Edwards, T.E., Ferre-D'Amare, A.R.

(2006) Structure 14: 1459-1468

• PubMed: 16962976 
• DOI: 10.1016/j.str.2006.07.008
• Primary Citation of Related Structures:  
  2HOJ, 2HOK, 2HOL, 2HOM, 2HOO, 2HOP


• PubMed Abstract: 
  

Riboswitches are noncoding mRNA elements that bind small-molecule metabolites with high affinity and specificity, and they regulate the expression of associated genes. The thi-box riboswitch can exhibit a 1000-fold higher affinity for thiamine pyrophosphate over closely related noncognate compounds such as thiamine monophosphate. To understand the chemical basis of thi-box pyrophosphate specificity, we have determined crystal structures of an E. coli thi-box bound to thiamine pyrophosphate, thiamine monophosphate, and the structural analogs benfotiamine and pyrithiamine. When bound to monophosphorylated compounds, the RNA elements that recognize the thiamine and phosphate moieties of the ligand move closer together. This allows the riboswitch to recognize the monophosphate in a manner similar to how it recognizes the beta-phosphate of thiamine pyrophosphate. In the pyrithiamine complex, the pyrophosphate binding site is largely unstructured. These results show how the riboswitch can bind to various metabolites, and why the thi-box preferentially binds thiamine pyrophosphate.

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Organizational Affiliation: 

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
thi-box riboswitch	A	83	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	P [auth A]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
BA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
CA	K [auth A], L [auth A], M [auth A], N [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.244 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.5	α = 90
b = 65.5	β = 90
c = 101.7	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-14 
• Released Date: 2006-09-19 
Deposition Author(s): Edwards, T.E., Ferre-D'Amare, A.R.

Revision History  

• Version 1.0: 2006-09-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance