6FZ0

Crystal structure of the metY SAM V riboswitch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

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Literature

Structure and ligand binding of the SAM-V riboswitch.

Huang, L.Lilley, D.M.J.

(2018) Nucleic Acids Res 46: 6869-6879

  • DOI: https://doi.org/10.1093/nar/gky520
  • Primary Citation of Related Structures:  
    6FZ0

  • PubMed Abstract: 

    SAM-V is one of the class of riboswitches that bind S-adenosylmethione, regulating gene expression by controlling translation. We have solved the crystal structure of the metY SAM-V riboswitch bound to its SAM ligand at 2.5 Å resolution. The RNA folds as an H-type pseudoknot, with a major-groove triple helix in which resides the SAM ligand binding site. The bound SAM adopts an elongated conformation aligned with the axis of the triple helix, and is held at either end by hydrogen bonding to the adenine and the amino acid moieties. The central sulfonium cation makes electrostatic interactions with an U:A.U base triple, so conferring specificity. We propose a model in which SAM binding leads to association of the triplex third strand that stabilizes a short helix and occludes the ribosome binding site. Thus the new structure explains both ligand specificity and the mechanism of genetic control.


  • Organizational Affiliation

    Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
metY SAM V (53-MER)53Candidatus Pelagibacter ubique HTCC1062
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.828α = 90
b = 87.828β = 90
c = 62.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomA18604

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references