Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48384.62 
• Atom Count: 2944 
• Residue Count: 420 
• Unique protein chains: 1

4YP1

Misting with CDA

• DOI: 10.2210/pdb4YP1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli


• Deposited: 2015-03-12 Released: 2015-10-07 
• Deposition Author(s): Chin, K.H., Chen, C.K., Tu, Z.I., Chou, S.H.
• Funding Organization(s): Ministry of Education 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.260 
• R-Value Work: 0.210 

Literature

Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK.

Chin, K.H., Liang, J.M., Yang, J.G., Shih, M.S., Tu, Z.L., Wang, Y.C., Sun, X.H., Hu, N.J., Liang, Z.X., Dow, J.M., Ryan, R.P., Chou, S.H.

(2015) Biochemistry 54: 4936-4951

• PubMed: 26171638 
• DOI: 10.1021/acs.biochem.5b00633
• Primary Citation of Related Structures:  
  5F29


• PubMed Abstract: 
  

Cyclic di-AMP (c-di-AMP) is a relatively new member of the family of bacterial cyclic dinucleotide second messengers. It has attracted significant attention in recent years because of the abundant roles it plays in a variety of Gram-positive bacteria. The structural features that allow diverse bacterial proteins to bind c-di-AMP are not fully understood. Here we report the biophysical and structural studies of c-di-AMP in complex with a bacterial cation-proton antiporter (CpaA) RCK (regulator of the conductance of K(+)) protein from Staphylococcus aureus (Sa). The crystal structure of the SaCpaA_RCK C-terminal domain (CTD) in complex with c-di-AMP was determined to a resolution of 1.81 Å. This structure revealed two well-liganded water molecules, each interacting with one of the adenine bases by a unique H2Olp-π interaction to stabilize the complex. Sequence blasting using the SaCpaA_RCK primary sequence against the bacterial genome database returned many CpaA analogues, and alignment of these sequences revealed that the active site residues are all well-conserved, indicating a universal c-di-AMP binding mode for CpaA_RCK. A proteoliposome activity assay using the full-length SaCpaA membrane protein indicated that c-di-AMP binding alters its antiporter activity by approximately 40%. A comparison of this structure to all other reported c-di-AMP-receptor complex structures revealed that c-di-AMP binds to receptors in either a "U-shape" or "V-shape" mode. The two adenine rings are stabilized in the inner interaction zone by a variety of CH-π, cation-π, backbone-π, or H2Olp-π interaction, but more commonly in the outer interaction zone by hydrophobic CH-π or π-π interaction. The structures determined to date provide an understanding of the mechanisms by which a single c-di-AMP can interact with a variety of receptor proteins, and how c-di-AMP binds receptor proteins in a special way different from that of c-di-GMP.

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Organizational Affiliation: 

†National Chung Hsing University Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, ROC.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Stimulator of interferon genes protein	A, B	210	Mus musculus	Mutation(s): 0  Gene Names: Tmem173 (Eris Mita, Mpys, Sting)
Find proteins for Q3TBT3 (Mus musculus) Go to UniProtKB:  Q3TBT3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.260 
• R-Value Work: 0.210 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 45.427	α = 90.00
b = 48.208	β = 90.00
c = 172.420	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
CNS	phasing
CNS	refinement
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-03-12 
• Released Date: 2015-10-07 
• Deposition Author(s): Chin, K.H., Chen, C.K., Tu, Z.I., Chou, S.H.

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Funding Organization	Location	Grant Number
Ministry of Education	Taiwan	102-2113-M-005-006-MY3

Revision History 

• Version 1.0: 2015-10-07
  Type: Initial release