3K1V

Cocrystal structure of a mutant class-I preQ1 riboswitch

• PDB DOI: https://doi.org/10.2210/pdb3K1V/pdb
• Entry: 3K1V supersedes: 3FU4
• NAKB: 3K1V

• Classification: RNA
• Mutation(s): No 


• Deposited: 2009-09-28 Released: 2009-10-06 
• 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: 2.20 Å
• R-Value Free: 
  0.269 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

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

• PubMed: 19234468 
• DOI: https://doi.org/10.1038/nsmb.1563
• Primary Citation of 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.

Macromolecule Content

• Total Structure Weight: 11.18 kDa 
• Atom Count: 693 
• Modelled Residue Count: 30 
• Deposited Residue Count: 34 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.269 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.81	α = 90
b = 76.81	β = 90
c = 85.9	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Klein, D.J., Edwards, T.E., Ferre-D'Amare, A.R.
• This entry supersedes: 3FU4

Revision History  

• Version 1.0: 2009-10-06
  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