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- PDB-8ik0: Cryo-EM structure of Stimulator of interferon genes -

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Basic information

Entry
Database: PDB / ID: 8ik0
TitleCryo-EM structure of Stimulator of interferon genes
ComponentsStimulator of interferon genes protein,Immune protein Tsi3
KeywordsIMMUNE SYSTEM / adaptor protein
Function / homology
Function and homology information


STING mediated induction of host immune responses / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / cGAS/STING signaling pathway / reticulophagy / autophagosome membrane / autophagosome assembly / positive regulation of macroautophagy / autophagosome ...STING mediated induction of host immune responses / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / cGAS/STING signaling pathway / reticulophagy / autophagosome membrane / autophagosome assembly / positive regulation of macroautophagy / autophagosome / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of interferon-beta production / Neutrophil degranulation / protein complex oligomerization / cytoplasmic vesicle / defense response to virus / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm / protein homodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
: / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Stimulator of interferon genes protein / Immune protein Tsi3
Similarity search - Component
Biological speciesGallus gallus (chicken)
Pseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLu, D.F. / Shang, G.J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2301400 China
CitationJournal: Mol Cell / Year: 2023
Title: The mechanism of STING autoinhibition and activation.
Authors: Sheng Liu / Bo Yang / Yingxiang Hou / Kaige Cui / Xiaozhu Yang / Xiaoxiong Li / Lianwan Chen / Shichao Liu / Zhichao Zhang / Yuanyuan Jia / Yufeng Xie / Ying Xue / Xiaomei Li / Bingxue Yan / ...Authors: Sheng Liu / Bo Yang / Yingxiang Hou / Kaige Cui / Xiaozhu Yang / Xiaoxiong Li / Lianwan Chen / Shichao Liu / Zhichao Zhang / Yuanyuan Jia / Yufeng Xie / Ying Xue / Xiaomei Li / Bingxue Yan / Changxin Wu / Wen Deng / Jianxun Qi / Defen Lu / George F Gao / Peiyi Wang / Guijun Shang /
Abstract: 2',3'-cGAMP, produced by the DNA sensor cGAS, activates stimulator of interferon genes (STING) and triggers immune response during infection. Tremendous effort has been placed on unraveling the ...2',3'-cGAMP, produced by the DNA sensor cGAS, activates stimulator of interferon genes (STING) and triggers immune response during infection. Tremendous effort has been placed on unraveling the mechanism of STING activation. However, little is known about STING inhibition. Here, we found that apo-STING exhibits a bilayer with head-to-head as well as side-by-side packing, mediated by its ligand-binding domain (LBD). This type of assembly holds two endoplasmic reticulum (ER) membranes together not only to prevent STING ER exit but also to eliminate the recruitment of TBK1, representing the autoinhibited state of STING. Additionally, we obtained the filament structure of the STING/2',3'-cGAMP complex, which adopts a bent monolayer assembly mediated by LBD and transmembrane domain (TMD). The active, curved STING polymer could deform ER membrane to support its ER exit and anterograde transportation. Our data together provide a panoramic vision regarding STING autoinhibition and activation, which adds substantially to current understanding of the cGAS-STING pathway.
History
DepositionFeb 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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,Immune protein Tsi3
B: Stimulator of interferon genes protein,Immune protein Tsi3
C: Stimulator of interferon genes protein,Immune protein Tsi3
F: Stimulator of interferon genes protein,Immune protein Tsi3
D: Stimulator of interferon genes protein,Immune protein Tsi3
G: Stimulator of interferon genes protein,Immune protein Tsi3
E: Stimulator of interferon genes protein,Immune protein Tsi3
H: Stimulator of interferon genes protein,Immune protein Tsi3


Theoretical massNumber of molelcules
Total (without water)442,2598
Polymers442,2598
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Stimulator of interferon genes protein,Immune protein Tsi3 / / STING / Transmembrane protein 173 / Anti-toxin protein Tsi3


Mass: 55282.332 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: STING1, STING, TMEM173, tsi3, PA3485 / Production host: Homo sapiens (human) / References: UniProt: E1C7U0, UniProt: Q9HYC4

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: fiber of adaptor protein / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Gallus gallus (chicken)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Details: 20mM HEPES, 150mM NaCl, 1mM TCEP, 0.03% DDM/CHS(5:1)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1057869 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00219932
ELECTRON MICROSCOPYf_angle_d0.55127076
ELECTRON MICROSCOPYf_dihedral_angle_d3.6362756
ELECTRON MICROSCOPYf_chiral_restr0.0373196
ELECTRON MICROSCOPYf_plane_restr0.0053384

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