Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42 kDa 
• Atom Count: 2,847 
• Modelled Residue Count: 185 
• Deposited Residue Count: 192 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 3UCZ

The c-di-GMP-I riboswitch bound to GpG

• PDB DOI:  https://doi.org/10.2210/pdb3UCZ/pdb
• NDB: NA1366

• Classification: SIGNALING PROTEIN/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2011-10-27 Released: 2012-01-04 
• Deposition Author(s): Smith, K.D., Strobel, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.202 
• R-Value Observed: 0.206 

Literature

Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer.

Smith, K.D., Lipchock, S.V., Strobel, S.A.

(2012) Biochemistry 51: 425-432

• PubMed: 22148472 
• DOI: https://doi.org/10.1021/bi2016662
• Primary Citation of Related Structures:  
  3UCU, 3UCZ, 3UD3, 3UD4


• PubMed Abstract: 
  

The cyclic dinucleotide c-di-GMP regulates lifestyle transitions in many bacteria, such as the change from a free motile state to a biofilm-forming community. Riboswitches that bind this second messenger are important downstream targets in this bacterial signaling pathway. The breakdown of c-di-GMP in the cell is accomplished enzymatically and results in the linear dinucleotide pGpG. The c-di-GMP-binding riboswitches must be able to discriminate between their cognate cyclic ligand and linear dinucleotides in order to be selective biological switches. It has been reported that the c-di-GMP-I riboswitch binds c-di-GMP 5 orders of magnitude better than the linear pGpG, but the cause of this large energetic difference in binding is unknown. Here we report binding data and crystal structures of several linear c-di-GMP analogues in complex with the c-di-GMP-I riboswitch. These data reveal the parameters for phosphate recognition and the structural basis of linear dinucleotide binding to the riboswitch. Additionally, the pH dependence of binding shows that exclusion of pGpG is not due to the additional negative charge on the ligand. These data reveal principles that, along with published work, will contribute to the design of c-di-GMP analogues with properties desirable for use as chemical tools and potential therapeutics.

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Organizational Affiliation: 

Department of Chemistry, Yale University, New Haven, Connecticut 06520-8321, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U1 small nuclear ribonucleoprotein A	A [auth P]	98	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Length	Organism	Image
RNA (92-MER)	B [auth R]	92	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*G)-3')	C [auth D]	2	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth P], E [auth R], F [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.202 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.808	α = 90
b = 45.358	β = 95.81
c = 77.334	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-04 
Deposition Author(s): Smith, K.D., Strobel, S.A.

Revision History  

• Version 1.0: 2012-01-04
  Type: Initial release
  
• Version 1.1: 2012-10-17
  Changes: Database references