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- PDB-9n7f: HsSTING with cGAMP/C53/DCA -

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Basic information

Entry
Database: PDB / ID: 9n7f
TitleHsSTING with cGAMP/C53/DCA
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / Innate immunity / membrane protein
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / cGAS/STING signaling pathway ...STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / cGAS/STING signaling pathway / proton channel activity / reticulophagy / pattern recognition receptor signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / protein complex oligomerization / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / : / cellular response to interferon-beta / positive regulation of type I interferon production / positive regulation of defense response to virus by host / endoplasmic reticulum-Golgi intermediate compartment membrane / signaling adaptor activity / antiviral innate immune response / activation of innate immune response / positive regulation of interferon-beta production / autophagosome / protein serine/threonine kinase binding / Regulation of innate immune responses to cytosolic DNA / secretory granule membrane / cytoplasmic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / peroxisome / regulation of inflammatory response / defense response to virus / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / cilium / ciliary basal body / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / protein kinase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain
Similarity search - Domain/homology
cGAMP / Chem-9IM / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsGharpure, A. / Ward, A.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI182439-01A1 United States
CitationJournal: To Be Published
Title: Microbiota-derived secondary bile acids promote STING activation and antitumor activity
Authors: Yang, X. / Zhang, X. / Li, W. / Gharpure, A. / Hansel, A. / Tillack, A. / Wu, C. / Hsieh, Y. / Sulpizio, A. / Dikiy, S. / Zhao, X. / Forli, S. / Ward, A.B. / Parker, C.G. / Hang, H.C.
History
DepositionFeb 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stimulator of interferon genes protein
B: Stimulator of interferon genes protein
C: Stimulator of interferon genes protein
D: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,3158
Polymers160,9844
Non-polymers2,3314
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Stimulator of interferon genes protein / hSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / hMITA / ...hSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / hMITA / Transmembrane protein 173


Mass: 40246.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING1, ERIS, MITA, STING, TMEM173 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q86WV6
#2: Chemical ChemComp-9IM / 1-[(2-chloro-6-fluorophenyl)methyl]-3,3-dimethyl-2-oxo-N-[(2,4,6-trifluorophenyl)methyl]-2,3-dihydro-1H-indole-6-carboxamide


Mass: 490.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H19ClF4N2O2
#3: Chemical ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Stimulator of interferon genes / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.40 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2150 mMSodium ChlorideNaCl1
30.5 mMTCEPC9H15O6P1
40.02 %Dodecyl maltosideC24H46O111
50.004 %Cholesteryl hemisuccinateC31H50O41
60.1 mMDeoxycholic acidC24H40O41
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: OTHER / Nominal magnification: 190000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 20 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3.2 sec. / Electron dose: 45.12 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of real images: 5839

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 284997 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7SII

7sii


Accession code: 7SII / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.93 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210546
ELECTRON MICROSCOPYf_angle_d0.53214354
ELECTRON MICROSCOPYf_dihedral_angle_d4.0771448
ELECTRON MICROSCOPYf_chiral_restr0.0371594
ELECTRON MICROSCOPYf_plane_restr0.0051814

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