3FU2 | pdb_00003fu2

Cocrystal structure of a class-I preQ1 riboswitch

• PDB DOI: https://doi.org/10.2210/pdb3FU2/pdb
• NAKB: 3FU2

• Classification: RNA
• Mutation(s): No 


• Deposited: 2009-01-13 Released: 2009-03-03 
• Deposition Author(s): Klein, D.J., Edwards, T.E., Ferre-D'Amare, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.267 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.206 (DCC) 

Literature

Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase

Klein, D.J., Edwards, T.E., Ferre-D'Amare, A.R.

(2009) Nat Struct Mol Biol 16: 343-344

• PubMed: 19234468 
• DOI: https://doi.org/10.1038/nsmb.1563
• Primary Citation Related Structures: 
  3FU2, 3K1V


• PubMed Abstract: 
  

  Riboswitches are mRNA domains that bind metabolites and modulate gene expression in cis. We report cocrystal structures of a remarkably compact riboswitch (34 nucleotides suffice for ligand recognition) from Bacillus subtilis that is selective for the essential nucleobase preQ(1) (7-aminomethyl-7-deazaguanine). The structures reveal a previously unrecognized pseudoknot fold and suggest a conserved gene-regulatory mechanism whereby ligand binding promotes sequestration of an RNA segment that otherwise assembles into a transcriptional antiterminator.

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Organizational Affiliation: 
• Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.4 kDa 
• Atom Count: 2,057 
• Modeled Residue Count: 97 
• Deposited Residue Count: 102 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
PreQ1 riboswitch	A, B, C	34	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRF	D [auth A], J [auth B], M [auth C]	7-DEAZA-7-AMINOMETHYL-GUANINE C7 H9 N5 O MEYMBLGOKYDGLZ-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], N [auth C], O [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.267 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.206 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.208	α = 90
b = 78.208	β = 90
c = 85.22	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Klein, D.J., Edwards, T.E., Ferre-D'Amare, A.R.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations