Biological Assembly 1  

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Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42670.75 
• Atom Count: 2708 
• Residue Count: 122 
• Unique nucleic acid chains: 1

4QKA

c-di-AMP riboswitch from Thermoanaerobacter pseudethanolicus, iridium hexamine soak

• DOI: 10.2210/pdb4QKA/pdb
• NDB: NA3047

• Classification: RNA


• Deposited: 2014-06-05 Released: 2014-08-06 
• Deposition Author(s): Gao, A., Serganov, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.2 Å
• R-Value Free: 0.197 
• R-Value Work: 0.171 

Literature

Structural insights into recognition of c-di-AMP by the ydaO riboswitch.

Gao, A., Serganov, A.

(2014) Nat.Chem.Biol. 10: 787-792

• PubMed: 25086507 
• DOI: 10.1038/nchembio.1607
• Primary Citation of Related Structures:  
  4QK9, 4QK8


• PubMed Abstract: 
  

Bacterial second messenger cyclic di-AMP (c-di-AMP) is implicated in signaling DNA damage and cell wall stress through interactions with several protein receptors and a widespread ydaO-type riboswitch. We report the crystal structures of c-di-AMP riboswitches from Thermoanaerobacter pseudethanolicus and Thermovirga lienii determined at ∼3.0-Å resolution. In both species, the RNA adopts an unforeseen 'square'-shaped pseudosymmetrical architecture that features two three-way junctions, a turn and a pseudoknot, positioned in the square corners. Uncharacteristically for riboswitches, the structure is stapled by two ligand molecules that span the interior of the structure and employ similar noncanonical interactions for RNA recognition. Mutations in either ligand-binding site negatively affect c-di-AMP binding, suggesting that the riboswitch-triggered genetic response requires contribution of both ligands. Our data provide what are to our knowledge the first insights into specific sensing of c-di-AMP and a molecular mechanism underlying the common c-di-AMP-dependent control of essential cellular processes in bacteria.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
C-di-AMP riboswitch	A	122	N/A

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
2BA	A	(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate C20 H24 N10 O12 P2 PDXMFTWFFKBFIN-XPWFQUROSA-N
IRI	A	IRIDIUM HEXAMMINE ION H18 Ir N6 CGMAOQLDNKCXGK-RIUFHJFFAL

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
23G	A	RNA OH 3 prime terminus	C10 H13 N5 O10 P2		G
GTP	A	NON-POLYMER	C10 H16 N5 O14 P3		G

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.2 Å
• R-Value Free: 0.197 
• R-Value Work: 0.171 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 116.035	α = 90.00
b = 116.035	β = 90.00
c = 114.098	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	phasing
ADSC	data collection
HKL-2000	data scaling
PHENIX	refinement
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-05 
• Released Date: 2014-08-06 
• Deposition Author(s): Gao, A., Serganov, A.

Revision History 

• Version 1.0: 2014-08-06
  Type: Initial release
• Version 1.1: 2014-08-27
  Type: Database references
• Version 1.2: 2014-09-10
  Type: Database references