9JW6 | pdb_00009jw6

STING bound with a novel small molecule agonist


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9JW6

This is version 1.1 of the entry. See complete history

Literature

A chemical agonist and the Golgi-resident lipid PI4P activate STING by inducing transmembrane helix rearrangement.

Han, J.Zhang, S.Hou, Y.Wang, Y.Zhang, Z.Yang, J.Xu, Y.Peng, Z.Yin, H.Chen, K.Liu, X.Zhang, C.

(2026) Immunity 59: 34-47.e9

  • DOI: https://doi.org/10.1016/j.immuni.2025.11.004
  • Primary Citation Related Structures: 
    9JW6

  • PubMed Abstract: 

    The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway is critical in innate immunity. Recent research has highlighted the importance of phosphatidylinositol 4-phosphate (PI4P) signaling within the Golgi apparatus for STING activation. However, the exact molecular mechanisms by which PI4P regulates STING have remained unclear. Here, we report the activation mechanism of STING triggered by PI4P and a chemical STING agonist, GNE-6468. Utilizing cryoelectron microscopy, we determined that GNE-6468 bound to a distinct pocket within the STING transmembrane (TM) domain, promoting outward movements of the STING TM3 helix without altering the conformation of the ligand-binding domain. Notably, we provided structural insights into STING bound to both PI4P and GNE-6468, and they collectively induced STING oligomerization and STING-mediated immune responses. Functional assays further confirmed that the interactions among STING, PI4P, and GNE-6468 were essential for STING activation. Collectively, these results demonstrate that PI4P and GNE-6468 cooperatively bind STING to activate its signaling, highlighting its therapeutic potential.


  • Organizational Affiliation
    • School of Pharmaceutical Sciences, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China; SXMU-Tsinghua, Taiyuan, China.

Macromolecule Content 

  • Total Structure Weight: 150.66 kDa 
  • Atom Count: 9,700 
  • Modeled Residue Count: 1,212 
  • Deposited Residue Count: 1,324 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Stimulator of interferon genes protein
A, B, C, D
331Homo sapiensMutation(s): 0 
Gene Names: STING1ERISMITASTINGTMEM173
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV6 (Homo sapiens)
Explore Q86WV6 
Go to UniProtKB:  Q86WV6
PHAROS:  Q86WV6
GTEx:  ENSG00000184584 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86WV6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EER

Query on A1EER



Download:Ideal Coordinates CCD File
F [auth B],
H [auth D]
[(2R)-2-dodecanoyloxy-3-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] dodecanoate
C33 H64 O16 P2
XDBDEBIYNKTSHI-LJPZONEXSA-N
A1EDL

Query on A1EDL



Download:Ideal Coordinates CCD File
E [auth B],
G [auth D]
4-[6-(2-chloranyl-6-cyclopropyl-phenyl)carbonylimidazo[1,5-a]pyrimidin-8-yl]-2-oxidanyl-benzoic acid
C23 H16 Cl N3 O4
GIYKJPISDNWSJD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2026-04-29
    Changes: Data collection, Database references