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- EMDB-0505: Cryo-EM structure of full-length chicken STING in the cGAMP-bound... -

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Basic information

Entry
Database: EMDB / ID: 0505
TitleCryo-EM structure of full-length chicken STING in the cGAMP-bound tetrameric state
Map dataprimary map
Samplefull-length chicken STING:
Stimulator of interferon genes protein / ligand
Function / homologyStimulator of interferon genes protein, C-terminal / Neutrophil degranulation / Stimulator of interferon genes protein, C-terminal domain superfamily / STAT6-mediated induction of chemokines / Regulation of innate immune responses to cytosolic DNA / STING mediated induction of host immune responses / Transmembrane protein 173 / Stimulator of interferon genes protein / cyclic-GMP-AMP binding / interferon-beta production ...Stimulator of interferon genes protein, C-terminal / Neutrophil degranulation / Stimulator of interferon genes protein, C-terminal domain superfamily / STAT6-mediated induction of chemokines / Regulation of innate immune responses to cytosolic DNA / STING mediated induction of host immune responses / Transmembrane protein 173 / Stimulator of interferon genes protein / cyclic-GMP-AMP binding / interferon-beta production / cyclic-di-GMP binding / cytoplasmic pattern recognition receptor signaling pathway in response to virus / cellular response to interferon-beta / cellular response to exogenous dsRNA / positive regulation of defense response to virus by host / positive regulation of type I interferon production / peroxisome / regulation of inflammatory response / defense response to virus / positive regulation of DNA-binding transcription factor activity / mitochondrial outer membrane / positive regulation of protein binding / transcription factor binding / endoplasmic reticulum membrane / innate immune response / ubiquitin protein ligase binding / protein kinase binding / Golgi apparatus / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / integral component of membrane / Stimulator of interferon genes protein
Function and homology information
SourceGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / 6.5 Å resolution
AuthorsShang G / Zhang C / Chen ZJ / Bai X / Zhang X
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
Validation ReportPDB-ID: 6nt8

SummaryFull reportAbout validation report
DateDeposition: Jan 28, 2019 / Header (metadata) release: Mar 6, 2019 / Map release: Mar 6, 2019 / Last update: Mar 20, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nt8
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0505.map.gz (map file in CCP4 format, 40311 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
216 pix
0.84 Å/pix.
= 181.44 Å
216 pix
0.84 Å/pix.
= 181.44 Å
216 pix
0.84 Å/pix.
= 181.44 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 Level:0.015 (by author), 0.015 (movie #1):
Minimum - Maximum-0.015100539 - 0.03823336
Average (Standard dev.)0.0007007503 (0.0032038286)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions216216216
Origin0.00.00.0
Limit215.0215.0215.0
Spacing216216216
CellA=B=C: 181.43999 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z181.440181.440181.440
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.0150.0380.001

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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: 3

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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: 4 / Recombinant expression: No
MassTheoretical: 44.20707 kDa
SourceSpecies: Gallus gallus (chicken)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, cGAMP

LigandName: cGAMPCyclic guanosine monophosphate–adenosine monophosphate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.674411 kDa

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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: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
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: C1 (asymmetric) / Number of projections: 41033
3D reconstructionSoftware: RELION / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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