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- EMDB-61849: STING bound with a novel small molecule agonist -

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Basic information

Entry
Database: EMDB / ID: EMD-61849
TitleSTING bound with a novel small molecule agonist
Map data
Sample
  • Complex: STING bound with a novel small molecule agonist
    • Protein or peptide: Stimulator of interferon genes protein
  • Ligand: 4-[6-(2-chloranyl-6-cyclopropyl-phenyl)carbonylimidazo[1,5-a]pyrimidin-8-yl]-2-oxidanyl-benzoic acid
  • Ligand: [(2R)-2-dodecanoyloxy-3-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] dodecanoate
Keywordsendoplasmic reticulum / cyclic dinucleotides / signaling / adaptor protein / 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 / pattern recognition receptor signaling pathway / reticulophagy / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / protein complex oligomerization / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / positive regulation of DNA-binding transcription factor activity / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / antiviral innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / Regulation of innate immune responses to cytosolic DNA / protein serine/threonine kinase binding / positive regulation of interferon-beta production / autophagosome / cytoplasmic vesicle membrane / secretory granule 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 / endoplasmic reticulum membrane / protein kinase binding / 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
Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsHan J / Zhang S / Hou Y / Wang Y / Zhang Z / Yang J / Chen K / Liu X / Zhang C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of STING binding with phospholipid PI4P and activation by a molecule targeting a new pocket
Authors: Han J / Zhang S / Hou Y / Wang Y / Zhang Z / Yang J / Chen K / Liu X / Zhang C
History
DepositionOct 9, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61849.png

Downloads & links

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Map

FileDownload / File: emd_61849.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.2337642 - 5.4506745
Average (Standard dev.)0.00035401847 (±0.100374915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61849_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61849_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : STING bound with a novel small molecule agonist

EntireName: STING bound with a novel small molecule agonist
Components
  • Complex: STING bound with a novel small molecule agonist
    • Protein or peptide: Stimulator of interferon genes protein
  • Ligand: 4-[6-(2-chloranyl-6-cyclopropyl-phenyl)carbonylimidazo[1,5-a]pyrimidin-8-yl]-2-oxidanyl-benzoic acid
  • Ligand: [(2R)-2-dodecanoyloxy-3-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] dodecanoate

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Supramolecule #1: STING bound with a novel small molecule agonist

SupramoleculeName: STING bound with a novel small molecule agonist / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Stimulator of interferon genes protein

MacromoleculeName: Stimulator of interferon genes protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.058645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LHPSIPCPRG HGAQKAALVL LSACLVTLWG LGEPPEHTLR YLVLHLASLQ LGLLLNGVCS LAEELRHIHS RYRGSYWRTV RACLGCPLR RGALLLLSIY FYYSLPNAVG PPFTWMLALL GLSQALNILL GLKGLAPAEI SAVCEKGNFN VAHGLAWSYY I GYLRLILP ...String:
LHPSIPCPRG HGAQKAALVL LSACLVTLWG LGEPPEHTLR YLVLHLASLQ LGLLLNGVCS LAEELRHIHS RYRGSYWRTV RACLGCPLR RGALLLLSIY FYYSLPNAVG PPFTWMLALL GLSQALNILL GLKGLAPAEI SAVCEKGNFN VAHGLAWSYY I GYLRLILP ELQARIRTYN QHYNNLLRGA VSQRLYILLP LDCGVPDNLS MADPNIRFLD KLPQQTGDHA GIKDRVYSNS IY ELLENGQ RAGTCVLEYA TPLQTLFAMS QYSQAGFSRE DRLEQAKLFC RTLEDILADA PESQNNCRLI AYQEPADDSS FSL SQEVLR HLRQE

UniProtKB: Stimulator of interferon genes protein

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Macromolecule #2: 4-[6-(2-chloranyl-6-cyclopropyl-phenyl)carbonylimidazo[1,5-a]pyri...

MacromoleculeName: 4-[6-(2-chloranyl-6-cyclopropyl-phenyl)carbonylimidazo[1,5-a]pyrimidin-8-yl]-2-oxidanyl-benzoic acid
type: ligand / ID: 2 / Number of copies: 2 / Formula: A1EDL
Molecular weightTheoretical: 433.844 Da

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Macromolecule #3: [(2R)-2-dodecanoyloxy-3-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis...

MacromoleculeName: [(2R)-2-dodecanoyloxy-3-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] dodecanoate
type: ligand / ID: 3 / Number of copies: 2 / Formula: A1EER
Molecular weightTheoretical: 778.799 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM10
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 296029
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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