9DAW | pdb_00009daw

STING oligomer bound to cGAMP, C53 and PI(3,5)P2

PDB DOI: https://doi.org/10.2210/pdb9DAW/pdb
EM Map EMD-46700: EMDB EMDataResource

Classification: SIGNALING PROTEIN/ACTIVATOR
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-08-22 Released: 2025-12-17
Deposition Author(s): Jie, L., Zhang, X., Bai, X.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Welch Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for the roles of phosphoinositide phosphates and cholesterol in STING activation

Jie, L., Zhang, X., Bai, X.

To be published.

Macromolecule Content

Total Structure Weight: 163.56 kDa
Atom Count: 10,504
Modeled Residue Count: 1,286
Deposited Residue Count: 1,416
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stimulator of interferon genes protein	A, B, C, D	354	Homo sapiens	Mutation(s): 0 Gene Names: STING1, ERIS, MITA, TMEM173
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86WV6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BBH (Subject of Investigation/LOI) Query on A1BBH Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain E [auth A]	E [auth A], J [auth C]	(2R)-3-{[(R)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl di[(9Z)-octadec-9-enoate] C₄₅ H₈₅ O₁₉ P₃ NCQJPYRCYOFNGI-BVBQJIMISA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth C]
1SY (Subject of Investigation/LOI) Query on 1SY Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C]	G [auth B], I [auth C]	cGAMP C₂₀ H₂₄ N₁₀ O₁₃ P₂ XRILCFTWUCUKJR-INFSMZHSSA-N		Interactions Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain G [auth B] Focus chain I [auth C]
9IM (Subject of Investigation/LOI) Query on 9IM Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth D] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D]	H [auth B], L [auth D]	1-[(2-chloro-6-fluorophenyl)methyl]-3,3-dimethyl-2-oxo-N-[(2,4,6-trifluorophenyl)methyl]-2,3-dihydro-1H-indole-6-carboxamide C₂₅ H₁₉ Cl F₄ N₂ O₂ OEBVYNULNKSONR-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain L [auth D] Interactions & Density Focus chain H [auth B] Focus chain L [auth D]
Y01 (Subject of Investigation/LOI) Query on Y01 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C]	F [auth A], K [auth C]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Jie, L.

Zhang, X.

Bai, X.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA273595
Welch Foundation	United States	I-1702
Welch Foundation	United States	I-1944