Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 22146.04 
• Atom Count: 1467 
• Residue Count: 68 
• Unique nucleic acid chains: 1

1Y27

G-riboswitch-guanine complex

• DOI: 10.2210/pdb1Y27/pdb
• NDB: UR0052

• Classification: RNA
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli


• Deposited: 2004-11-20 Released: 2004-12-28 
• Deposition Author(s): Serganov, A., Yuan, Y.R., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.264 
• R-Value Work: 0.232 

Literature

Structural Basis for Discriminative Regulation of Gene Expression by Adenine- and Guanine-Sensing mRNAs

Serganov, A., Yuan, Y.R., Pikovskaya, O., Polonskaia, A., Malinina, L., Phan, A.T., Hobartner, C., Micura, R., Breaker, R.R., Patel, D.J.

(2004) Chem.Biol. 11: 1729-1741

• PubMed: 15610857 
• DOI: 10.1016/j.chembiol.2004.11.018
• Primary Citation of Related Structures:  
  1Y26


• PubMed Abstract: 
  

Metabolite-sensing mRNAs, or "riboswitches," specifically interact with small ligands and direct expression of the genes involved in their metabolism. Riboswitches contain sensing "aptamer" modules, capable of ligand-induced structural changes, and downstream regions, harboring expression-controlling elements. We report the crystal structures of the add A-riboswitch and xpt G-riboswitch aptamer modules that distinguish between bound adenine and guanine with exquisite specificity and modulate expression of two different sets of genes. The riboswitches form tuning fork-like architectures, in which the prongs are held in parallel through hairpin loop interactions, and the internal bubble zippers up to form the purine binding pocket. The bound purines are held by hydrogen bonding interactions involving conserved nucleotides along their entire periphery. Recognition specificity is associated with Watson-Crick pairing of the encapsulated adenine and guanine ligands with uridine and cytosine, respectively.

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Organizational Affiliation: 

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
Bacillus subtilis xpt	X	68	Bacillus subtilis

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GUN	X	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GDP	X	RNA LINKING	C10 H15 N5 O11 P2		G
CCC	X	RNA LINKING	C9 H13 N3 O10 P2		C

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.264 
• R-Value Work: 0.232 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 41.632	α = 90.00
b = 50.878	β = 90.00
c = 217.439	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
CCP4	phasing
REFMAC	refinement
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-11-20 
• Released Date: 2004-12-28 
• Deposition Author(s): Serganov, A., Yuan, Y.R., Patel, D.J.

Revision History 

• Version 1.0: 2004-12-28
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description
• Version 2.0: 2019-02-27
  Type: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary