3OWZ

Crystal structure of glycine riboswitch, soaked in Iridium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1016/j.molcel.2010.11.026
  • Primary Citation of Related Structures:  
    3OWI, 3OWW, 3OWZ, 3OX0, 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 unbound states ...

    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
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Domain II of glycine riboswitch88N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
Domain II of glycine riboswitch88N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IRI
Query on IRI
Download Ideal Coordinates CCD File 
GA [auth B]
HA [auth B]
IA [auth B]
JA [auth B]
KA [auth B]
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A]
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL		 Ligand Interaction
GLY
Query on GLY
Download Ideal Coordinates CCD File 
C [auth A],
X [auth B]		GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
DA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
Y [auth B],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GLY PDBBind:  3OWZ Kd: 3500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.61α = 90
b = 82.61β = 90
c = 149.55γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-10-08
    Changes: Structure summary