3IRW

Structure of a c-di-GMP riboswitch from V. cholerae

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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Literature

Structural basis of ligand binding by a c-di-GMP riboswitch.

Smith, K.D., Lipchock, S.V., Ames, T.D., Wang, J., Breaker, R.R., Strobel, S.A.

(2009) Nat Struct Mol Biol 16: 1218-1223

  • DOI: 10.1038/nsmb.1702
  • Primary Citation of Related Structures:  
    3IRW

  • PubMed Abstract: 

    • The second messenger signaling molecule bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates many processes in bacteria, including motility, pathogenesis and biofilm formation. c-di-GMP-binding riboswitches are important downstream targets in this signaling pathway ...

    The second messenger signaling molecule bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates many processes in bacteria, including motility, pathogenesis and biofilm formation. c-di-GMP-binding riboswitches are important downstream targets in this signaling pathway. Here we report the crystal structure, at 2.7 A resolution, of a c-di-GMP riboswitch aptamer from Vibrio cholerae bound to c-di-GMP, showing that the ligand binds within a three-helix junction that involves base-pairing and extensive base-stacking. The symmetric c-di-GMP is recognized asymmetrically with respect to both the bases and the backbone. A mutant aptamer was engineered that preferentially binds the candidate signaling molecule c-di-AMP over c-di-GMP. Kinetic and structural data suggest that genetic regulation by the c-di-GMP riboswitch is kinetically controlled and that gene expression is modulated through the stabilization of a previously unidentified P1 helix, illustrating a direct mechanism for c-di-GMP signaling.

    Organizational Affiliation: 

    Department of Chemistry, Yale University, New Haven, Connecticut, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AA [auth P]98Homo sapiensMutation(s): 2 
Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09012
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
c-di-GMP RiboswitchB [auth R]92Vibrio cholerae
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E
Download Ideal Coordinates CCD File 
C [auth R]9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N		 Ligand Interaction
IRI
Query on IRI
Download Ideal Coordinates CCD File 
D [auth R],
E [auth R],
F [auth R],
G [auth R],
H [auth R],
D [auth R],
E [auth R],
F [auth R],
G [auth R],
H [auth R],
I [auth R],
J [auth R],
K [auth R],
L [auth R]
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
M [auth R],
N [auth R]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.461α = 90
b = 45.123β = 96.79
c = 76.573γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2009-11-10 
    • Deposition Author(s): Smith, K.D.

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations, Structure summary