Crystal structure of the cobalamin riboswitch regulatory element

Experimental Data Snapshot

  • Resolution: 3.43 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 

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B12 cofactors directly stabilize an mRNA regulatory switch.

Johnson, J.E.Reyes, F.E.Polaski, J.T.Batey, R.T.

(2012) Nature 492: 133-137

  • DOI: https://doi.org/10.1038/nature11607
  • Primary Citation of Related Structures:  
    4FRG, 4FRN, 4GMA

  • PubMed Abstract: 

    Structures of riboswitch receptor domains bound to their effector have shown how messenger RNAs recognize diverse small molecules, but mechanistic details linking the structures to the regulation of gene expression remain elusive. To address this, here we solve crystal structures of two different classes of cobalamin (vitamin B(12))-binding riboswitches that include the structural switch of the downstream regulatory domain. These classes share a common cobalamin-binding core, but use distinct peripheral extensions to recognize different B(12) derivatives. In each case, recognition is accomplished through shape complementarity between the RNA and cobalamin, with relatively few hydrogen bonding interactions that typically govern RNA-small molecule recognition. We show that a composite cobalamin-RNA scaffold stabilizes an unusual long-range intramolecular kissing-loop interaction that controls mRNA expression. This is the first, to our knowledge, riboswitch crystal structure detailing how the receptor and regulatory domains communicate in a ligand-dependent fashion to regulate mRNA expression.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0596, USA.

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Entity ID: 1
MoleculeChains LengthOrganismImage
Cobalamin riboswitch aptamer domain
A, B
102marine metagenome
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on I2A

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
C62 H88 Co N13 O15 P
Query on BA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.43 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.605α = 90
b = 81.833β = 90
c = 147.722γ = 90
Software Package:
Software NamePurpose
SCALAdata processing
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-12-26
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description