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- EMDB-35503: Cryo-EM structure of Stimulator of interferon genes -

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Basic information

Entry
Database: EMDB / ID: EMD-35503
TitleCryo-EM structure of Stimulator of interferon genes
Map data
Sample
  • Complex: fiber of adaptor protein
    • Protein or peptide: Stimulator of interferon genes protein,Immune protein Tsi3
Keywordsadaptor protein / IMMUNE SYSTEM
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 / protein complex oligomerization / positive regulation of macroautophagy / autophagosome membrane / autophagosome assembly ...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 / protein complex oligomerization / positive regulation of macroautophagy / autophagosome membrane / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / positive regulation of interferon-beta production / endoplasmic reticulum-Golgi intermediate compartment membrane / autophagosome / Neutrophil degranulation / 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
: / : / Type six secretion immunity 3 domain / : / 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 (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLu DF / Shang GJ
Funding support China, 1 items
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, 2023-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35503.png

Downloads & links

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Map

FileDownload / File: emd_35503.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.)
1.1 Å/pix.
x 256 pix.
= 280.32 Å		1.1 Å/pix.
x 256 pix.
= 280.32 Å		1.1 Å/pix.
x 256 pix.
= 280.32 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.339
Minimum - Maximum-2.9866452 - 4.323909
Average (Standard dev.)0.020000843 (±0.109440304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35503_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35503_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : fiber of adaptor protein

EntireName: fiber of adaptor protein
Components
  • Complex: fiber of adaptor protein
    • Protein or peptide: Stimulator of interferon genes protein,Immune protein Tsi3

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Supramolecule #1: fiber of adaptor protein

SupramoleculeName: fiber of adaptor protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: Stimulator of interferon genes protein,Immune protein Tsi3

MacromoleculeName: Stimulator of interferon genes protein,Immune protein Tsi3
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Molecular weightTheoretical: 55.282332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPQDPSTRSS PARLLIPEPR AGRARHAACV LLAVCFVVLF LSGEPLAPIT RRVCTQLAAL QLGVLLKGCC CLAEEIFHLH SRHHGSLWQ VLCSCFPPRW HLALLLVGGS AYLDPPEDNG HSPRLALTLS CLCQLLVLAL GLQKLSAVEV SELTESSKKN V AHGLAWSY ...String:
MPQDPSTRSS PARLLIPEPR AGRARHAACV LLAVCFVVLF LSGEPLAPIT RRVCTQLAAL QLGVLLKGCC CLAEEIFHLH SRHHGSLWQ VLCSCFPPRW HLALLLVGGS AYLDPPEDNG HSPRLALTLS CLCQLLVLAL GLQKLSAVEV SELTESSKKN V AHGLAWSY YIGYLKVVLP RLKECMEEIS RTNPMLRAHR DTWKLHILVP LGCDIWDDLE KADSNIQYLA DLPETILTRA GI KRRVYKH SLYVIRDKDN KLRPCVLEFA SPLQTLCAMS QDDCAAFSRE QRLEQARLFY RSLRDILGSS KECAGLYRLI AYE EPAEPE SHFLSGLILW HLQQQQREEY MVLEVLFQGP VDFDKTLTHP NGLVVERPVG FDARRSAEGF RFDEGGKLRN PRQL EVQRQ DAPPPPDLAS RRLGDGEARY KVEEDDGGSA GSEYRLWAAK PAGARWIVVS ASEQSEDGEP TFALAWALLE RARLQ SSHH HHHHHH

UniProtKB: Stimulator of interferon genes protein, Immune protein Tsi3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Details: 20mM HEPES, 150mM NaCl, 1mM TCEP, 0.03% DDM/CHS(5:1)
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6nt6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1057869
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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