7EBD | pdb_00007ebd

Bacterial STING in complex with c-di-GMP

• PDB DOI: https://doi.org/10.2210/pdb7EBD/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Prevotella corporis
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-03-09 Released: 2021-09-15 
• Deposition Author(s): Ko, T.-P., Wang, Y.-C., Yang, C.-S., Hou, M.-H., Chen, Y.
• Funding Organization(s): Academia Sinica (Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure and functional implication of bacterial STING.

Ko, T.-P., Wang, Y.-C., Yang, C.-S., Hou, M.-H., Chen, C.-J., Chiu, Y.-F., Chen, Y.

(2022) Nat Commun 13: 26-26

• PubMed: 35013136 
• DOI: https://doi.org/10.1038/s41467-021-26583-3
• Primary Citation Related Structures: 
  7EBD, 7EBL


• PubMed Abstract: 
  

  Mammalian innate immune sensor STING (STimulator of INterferon Gene) was recently found to originate from bacteria. During phage infection, bacterial STING sense c-di-GMP generated by the CD-NTase (cGAS/DncV-like nucleotidyltransferase) encoded in the same operon and signal suicide commitment as a defense strategy that restricts phage propagation. However, the precise binding mode of c-di-GMP to bacterial STING and the specific recognition mechanism are still elusive. Here, we determine two complex crystal structures of bacterial STING/c-di-GMP, which provide a clear picture of how c-di-GMP is distinguished from other cyclic dinucleotides. The protein-protein interactions further reveal the driving force behind filament formation of bacterial STING. Finally, we group the bacterial STING into two classes based on the conserved motif in β-strand lid, which dictate their ligand specificity and oligomerization mechanism, and propose an evolution-based model that describes the transition from c-di-GMP-dependent signaling in bacteria to 2'3'-cGAMP-dependent signaling in eukaryotes.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
Institute of New Drug Development, China Medical University, Taichung, 406, Taiwan.
Graduate Institute of Integrated Medicine, China Medical University, Taichung, 406, Taiwan.
Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, 404, Taiwan.
Institute of New Drug Development, China Medical University, Taichung, 406, Taiwan. [e-mail].
Research Center for Cancer Biology, China Medical University, Taichung, 406, Taiwan. [e-mail].
New Drug Development Center, China Medical University, Taichung, 406, Taiwan. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 38.07 kDa 
• Atom Count: 2,845 
• Modeled Residue Count: 316 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TIR-like domain-containing protein	A, B	161	Prevotella corporis	Mutation(s): 0  Gene Names: HMPREF3226_02659 EC: 3.2.2.5
UniProt
Find proteins for A0A133PTK7 (Prevotella corporis) Explore A0A133PTK7  Go to UniProtKB:  A0A133PTK7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E (Subject of Investigation/LOI)	E [auth B]	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) C20 H24 N10 O14 P2 PKFDLKSEZWEFGL-MHARETSRSA-N
ACT	C [auth A], D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.534	α = 90
b = 86.995	β = 90
c = 35.223	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Ko, T.-P., Wang, Y.-C., Yang, C.-S., Hou, M.-H., Chen, Y.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2022-01-19
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Refinement description, Structure summary