6LAZ

the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 6LAS - determined by Ren, A., Sun, A.  

Literature

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: 10.1038/s41467-019-13600-9
  • Primary Citation of Related Structures:  

  • 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 re ...

    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.,Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, Leopold Franzens University, Innsbruck, A6020, Austria.,Life Sciences Institute, Zhejiang University, 310058, Hangzhou, Zhejiang, China. aimingren@zju.edu.cn.,National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics and School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China.,Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, Leopold Franzens University, Innsbruck, A6020, Austria. ronald.micura@uibk.ac.at.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A
C, D, E
93Homo sapiensMutation(s): 3 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (55-MER)A,B55Bifidobacterium angulatum
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
E7X
Query on E7X

Download SDF File 
Download CCD File 
A, B
(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-hydroxyethyl)amino]-2-azaniumyl-butanoate
C16 H25 N7 O6
OHBJWDDPDJOYBP-OPYVMVOTSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
A, B
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.390α = 90.00
b = 85.348β = 105.46
c = 93.165γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-11-13 
  • Released Date: 2020-01-01 
  • Deposition Author(s): Ren, A., Sun, A.

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

Revision History 

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