8HY9

Bacterial STING from Riemerella anatipestifer in complex with 3'3'-c-di-GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 

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Literature

Structural insights into the regulation, ligand recognition, and oligomerization of bacterial STING.

Hou, M.H.Wang, Y.C.Yang, C.S.Liao, K.F.Chang, J.W.Shih, O.Yeh, Y.Q.Sriramoju, M.K.Weng, T.W.Jeng, U.S.Hsu, S.D.Chen, Y.

(2023) Nat Commun 14: 8519-8519

  • DOI: https://doi.org/10.1038/s41467-023-44052-x
  • Primary Citation of Related Structures:  
    8HWI, 8HWJ, 8HY8, 8HY9, 8HYN

  • PubMed Abstract: 

    The cyclic GMP-AMP synthase (cGAS)/stimulator of interferon gene (STING) signaling pathway plays a critical protective role against viral infections. Metazoan STING undergoes multilayers of regulation to ensure specific signal transduction. However, the mechanisms underlying the regulation of bacterial STING remain unclear. In this study, we determined the crystal structure of anti-parallel dimeric form of bacterial STING, which keeps itself in an inactive state by preventing cyclic dinucleotides access. Conformational transition between inactive and active states of bacterial STINGs provides an on-off switch for downstream signaling. Some bacterial STINGs living in extreme environment contain an insertion sequence, which we show codes for an additional long lid that covers the ligand-binding pocket. This lid helps regulate anti-phage activities. Furthermore, bacterial STING can bind cyclic di-AMP in a triangle-shaped conformation via a more compact ligand-binding pocket, forming spiral-shaped protofibrils and higher-order fibril filaments. Based on the differences between cyclic-dinucleotide recognition, oligomerization, and downstream activation of different bacterial STINGs, we proposed a model to explain structure-function evolution of bacterial STINGs.


  • Organizational Affiliation

    Genomics BioSci. & Tech. Co. Ltd., New Taipei, 221411, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CD-NTase-associated protein 12163Riemerella anatipestifer Yb2Mutation(s): 0 
Gene Names: KYF39_09390
EC: 3.2.2.5
UniProt
Find proteins for E4TDY5 (Riemerella anatipestifer (strain ATCC 11845 / DSM 15868 / JCM 9532 / NCTC 11014))
Explore E4TDY5 
Go to UniProtKB:  E4TDY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE4TDY5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E (Subject of Investigation/LOI)
Query on C2E

Download Ideal Coordinates CCD File 
B [auth A]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
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.51α = 90
b = 40.99β = 105.041
c = 36.196γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan109-2311-B241-001
Ministry of Science and Technology (MoST, Taiwan)Taiwan111-2311-B-039-001-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Database references