Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.17 kDa 
• Atom Count: 3036 
• Modelled Residue Count: 136 
• Deposited Residue Count: 136 
• Unique nucleic acid chains: 1

3SLM

Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine-5'-monophosphate

• PDB DOI: 10.2210/pdb3SLM/pdb

• Classification: RNA
• Mutation(s): No 


• Deposited: 2011-06-24 Released: 2011-08-17 
• Deposition Author(s): Pikovskaya, O., Polonskaia, A., Patel, D.J., Serganov, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.200 
• R-Value Observed: 0.205 

Literature

Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.

Pikovskaya, O., Polonskaia, A., Patel, D.J., Serganov, A.

(2011) Nat Chem Biol 7: 748-755

• PubMed: 21841796 
• DOI: 10.1038/nchembio.631
• Primary Citation of Related Structures:  
  3SKI, 3SKL, 3SKR, 3SKT, 3SKW, 3SKZ, 3SLM, 3SLQ


• PubMed Abstract: 
  

Purine riboswitches have an essential role in genetic regulation of bacterial metabolism. This family includes the 2'-deoxyguanosine (dG) riboswitch, which is involved in feedback control of deoxyguanosine biosynthesis. To understand the principles that define dG selectivity, we determined crystal structures of the natural Mesoplasma florum riboswitch bound to cognate dG as well as to noncognate guanosine, deoxyguanosine monophosphate and guanosine monophosphate. Comparison with related purine riboswitch structures reveals that the dG riboswitch achieves its specificity through modification of key interactions involving the nucleobase and rearrangement of the ligand-binding pocket to accommodate the additional sugar moiety. In addition, we observe new conformational changes beyond the junctional binding pocket extending as far as peripheral loop-loop interactions. It appears that re-engineering riboswitch scaffolds will require consideration of selectivity features dispersed throughout the riboswitch tertiary fold, and structure-guided drug design efforts targeted to junctional RNA scaffolds need to be addressed within such an expanded framework.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (68-MER)	A, B	68	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGP	C [auth A], L [auth B]	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P LTFMZDNNPPEQNG-KVQBGUIXSA-N
SIN	I [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	J [auth A], K [auth A], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DGP	PDBBind:  3SLM	Kd: 3.79e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.200 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.954	α = 90
b = 66.058	β = 117.95
c = 72.503	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-24 
• Released Date: 2011-08-17 
Deposition Author(s): Pikovskaya, O., Polonskaia, A., Patel, D.J., Serganov, A.A.

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2011-10-26
  Changes: Database references