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- EMDB-0503: Cryo-EM structure of full-length chicken STING in the apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-0503
TitleCryo-EM structure of full-length chicken STING in the apo state
Map data
Samplefull-length chicken STING:
Stimulator of interferon genes protein
Function / homology
Function and homology information


integral component of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane / interferon-beta production / cyclic-GMP-AMP binding / reticulophagy / cyclic-di-GMP binding / cellular response to interferon-beta / autophagosome membrane / cellular response to exogenous dsRNA / activation of innate immune response / positive regulation of defense response to virus by host ...integral component of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane / interferon-beta production / cyclic-GMP-AMP binding / reticulophagy / cyclic-di-GMP binding / cellular response to interferon-beta / autophagosome membrane / cellular response to exogenous dsRNA / activation of innate immune response / positive regulation of defense response to virus by host / integral component of endoplasmic reticulum membrane / autophagosome assembly / positive regulation of macroautophagy / autophagosome / positive regulation of type I interferon production / peroxisome / protein complex oligomerization / regulation of inflammatory response / defense response to virus / positive regulation of DNA-binding transcription factor activity / mitochondrial outer membrane / positive regulation of protein binding / endosome / transcription factor binding / endoplasmic reticulum membrane / ubiquitin protein ligase binding / innate immune response / protein kinase binding / Golgi apparatus / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / cytosol / cytoplasm
Stimulator of interferon genes protein, C-terminal domain superfamily / Stimulator of interferon genes protein, C-terminal / Stimulator of interferon genes protein
Stimulator of interferon genes protein / Stimulator of interferon genes protein
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsShang G / Zhang C / Chen ZJ / Bai X / Zhang X
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088197 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130289 United States
Welch FoundationI-1702 United States
Welch FoundationI-1389 United States
Welch FoundationI-1944 United States
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structures of STING reveal its mechanism of activation by cyclic GMP-AMP.
Authors: Guijun Shang / Conggang Zhang / Zhijian J Chen / Xiao-Chen Bai / Xuewu Zhang /
Abstract: Infections by pathogens that contain DNA trigger the production of type-I interferons and inflammatory cytokines through cyclic GMP-AMP synthase, which produces 2'3'-cyclic GMP-AMP (cGAMP) that binds ...Infections by pathogens that contain DNA trigger the production of type-I interferons and inflammatory cytokines through cyclic GMP-AMP synthase, which produces 2'3'-cyclic GMP-AMP (cGAMP) that binds to and activates stimulator of interferon genes (STING; also known as TMEM173, MITA, ERIS and MPYS). STING is an endoplasmic-reticulum membrane protein that contains four transmembrane helices followed by a cytoplasmic ligand-binding and signalling domain. The cytoplasmic domain of STING forms a dimer, which undergoes a conformational change upon binding to cGAMP. However, it remains unclear how this conformational change leads to STING activation. Here we present cryo-electron microscopy structures of full-length STING from human and chicken in the inactive dimeric state (about 80 kDa in size), as well as cGAMP-bound chicken STING in both the dimeric and tetrameric states. The structures show that the transmembrane and cytoplasmic regions interact to form an integrated, domain-swapped dimeric assembly. Closure of the ligand-binding domain, induced by cGAMP, leads to a 180° rotation of the ligand-binding domain relative to the transmembrane domain. This rotation is coupled to a conformational change in a loop on the side of the ligand-binding-domain dimer, which leads to the formation of the STING tetramer and higher-order oligomers through side-by-side packing. This model of STING oligomerization and activation is supported by our structure-based mutational analyses.
Validation ReportPDB-ID: 6nt6

SummaryFull reportAbout validation report
History
DepositionJan 28, 2019-
Header (metadata) releaseMar 6, 2019-
Map releaseMar 6, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nt6
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0503.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 168 pix.
= 141.12 Å
0.84 Å/pix.
x 168 pix.
= 141.12 Å
0.84 Å/pix.
x 168 pix.
= 141.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.05390041 - 0.08709491
Average (Standard dev.)0.00058112014 (±0.0046988046)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 141.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z141.120141.120141.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.0540.0870.001

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Supplemental data

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Sample components

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Entire full-length chicken STING

EntireName: full-length chicken STING / Number of components: 2

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Component #1: protein, full-length chicken STING

ProteinName: full-length chicken STING / Recombinant expression: No
SourceSpecies: Gallus gallus (chicken)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293 GnTI-

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Component #2: protein, Stimulator of interferon genes protein

ProteinName: Stimulator of interferon genes protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 44.20707 kDa
SourceSpecies: Gallus gallus (chicken)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 4.5 mg/mL / pH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 164337
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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