the wildtype SAM-VI riboswitch bound to SAM

Experimental Data Snapshot

  • Resolution: 2.71 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 

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Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6LAU 6LAX 6LAZ


SAM-VI riboswitch structure and signature for ligand discrimination.

Sun, A.Gasser, C.Li, F.Chen, H.Mair, S.Krasheninina, O.Micura, R.Ren, A.

(2019) Nat Commun 10: 5728-5728

  • DOI: https://doi.org/10.1038/s41467-019-13600-9
  • Primary Citation of Related Structures:  
    6LAS, 6LAU, 6LAX, 6LAZ

  • PubMed Abstract: 

    Riboswitches are metabolite-sensing, conserved domains located in non-coding regions of mRNA that are central to regulation of gene expression. Here we report the first three-dimensional structure of the recently discovered S-adenosyl-L-methionine responsive SAM-VI riboswitch. SAM-VI adopts a unique fold and ligand pocket that are distinct from all other known SAM riboswitch classes. The ligand binds to the junctional region with its adenine tightly intercalated and Hoogsteen base-paired. Furthermore, we reveal the ligand discrimination mode of SAM-VI by additional X-ray structures of this riboswitch bound to S-adenosyl-L-homocysteine and a synthetic ligand mimic, in combination with isothermal titration calorimetry and fluorescence spectroscopy to explore binding thermodynamics and kinetics. The structure is further evaluated by analysis of ligand binding to SAM-VI mutants. It thus provides a thorough basis for developing synthetic SAM cofactors for applications in chemical and synthetic RNA biology.

  • Organizational Affiliation

    Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AC,
D [auth E],
E [auth D]
93Homo sapiensMutation(s): 3 
Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
GTEx:  ENSG00000077312 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09012
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (55-MER)
A, B
55Bifidobacterium angulatum
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
D [auth E],
E [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.71 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.417α = 90
b = 84.214β = 105.79
c = 90.484γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31870810, 91640104 and 31670826

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release