2YDH | pdb_00002ydh

Crystal structure of the SAM-I riboswitch A94G U34 G18U G19U variant in complex with SAM

• PDB DOI: https://doi.org/10.2210/pdb2YDH/pdb
• NAKB: 2YDH

• Classification: RNA
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis
• Mutation(s): No 


• Deposited: 2011-03-21 Released: 2011-09-07 
• Deposition Author(s): Schroeder, K.T., Daldrop, P., Lilley, D.M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.321 (Depositor), 0.322 (DCC) 
• R-Value Work: 
  0.269 (Depositor), 0.272 (DCC) 
• R-Value Observed: 
  0.274 (Depositor) 

Starting Model: experimental

Literature

RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn.

Schroeder, K.T., Daldrop, P., Lilley, D.M.J.

(2011) Structure 19: 1233

• PubMed: 21893284 
• DOI: https://doi.org/10.1016/j.str.2011.07.003
• Primary Citation Related Structures: 
  2YDH, 2YGH


• PubMed Abstract: 
  

  The kink turn is a widespread RNA motif that introduces an acute kink into the axis of duplex RNA, typically comprising a bulge followed by a G⋅A and A⋅G pairs. The kinked conformation is stabilized by metal ions, or the binding of proteins including L7Ae. We now demonstrate a third mechanism for the stabilization of k-turn structure, involving tertiary interactions within a larger RNA structure. The SAM-I riboswitch contains an essential standard k-turn sequence that kinks a helix so that its terminal loop can make a long-range interaction. We find that some sequence variations in the k-turn within the riboswitch do not prevent SAM binding, despite preventing the folding of the k-turn in isolation. Furthermore, two crystal structures show that the sequence-variant k-turns are conventionally folded within the riboswitch. This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure.

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Organizational Affiliation: 
• Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 31.58 kDa 
• Atom Count: 2,058 
• Modeled Residue Count: 94 
• Deposited Residue Count: 94 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
SAM-I RIBOSWITCH	A	94	Caldanaerobacter subterraneus subsp. tengcongensis

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	G [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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.321 (Depositor), 0.322 (DCC) 
• R-Value Work:  0.269 (Depositor), 0.272 (DCC) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.899	α = 90
b = 61.899	β = 90
c = 157.628	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Schroeder, K.T., Daldrop, P., Lilley, D.M.J.

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2011-09-21
  Changes: Database references
• Version 1.2: 2016-09-28
  Changes: Structure summary
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description