3OX0

Crystal structure of glycine riboswitch, unbound state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.049 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch.

Huang, L.Serganov, A.Patel, D.J.

(2010) Mol.Cell 40: 774-786

  • DOI: 10.1016/j.molcel.2010.11.026
  • Primary Citation of Related Structures:  3OWI, 3OWW, 3OWZ, 3OXB, 3OXD, 3OXE, 3OXJ, 3OXM

  • PubMed Abstract: 
  • Glycine riboswitches regulate gene expression by feedback modulation in response to cooperative binding to glycine. Here, we report on crystal structures of the second glycine-sensing domain from the Vibrio cholerae riboswitch in the ligand-bound and ...

    Glycine riboswitches regulate gene expression by feedback modulation in response to cooperative binding to glycine. Here, we report on crystal structures of the second glycine-sensing domain from the Vibrio cholerae riboswitch in the ligand-bound and unbound states. This domain adopts a three-helical fold that centers on a three-way junction and accommodates glycine within a bulge-containing binding pocket above the junction. Glycine recognition is facilitated by a pair of bound Mg(2+) cations and governed by specific interactions and shape complementarity with the pocket. A conserved adenine extrudes from the binding pocket and intercalates into the junction implying that glycine binding in the context of the complete riboswitch could impact on gene expression by stabilizing the riboswitch junction and regulatory P1 helix. Analysis of riboswitch interactions in the crystal and footprinting experiments indicates that adjacent glycine-sensing modules of the riboswitch could form specific interdomain interactions, thereby potentially contributing to the cooperative response.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Domain II of glycine riboswitchA88N/A
Entity ID: 2
MoleculeChainsLengthOrganism
Domain II of glycine riboswitchB88N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
GDP
Query on GDP
A
RNA LINKINGC10 H15 N5 O11 P2G
CCC
Query on CCC
A, B
RNA LINKINGC9 H13 N3 O10 P2C
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.049 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.281α = 90.00
b = 84.281β = 90.00
c = 199.907γ = 120.00
Software Package:
Software NamePurpose
CBASSdata collection
REFMACphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance