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- EMDB-0502: Cryo-EM structure of full-length human STING in the apo state -

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Basic information

Entry
Database: EMDB / ID: 0502
TitleCryo-EM structure of full-length human STING in the apo state
Map dataFull-length human STING in the apo state
Samplefull-length human STING:
Stimulator of interferon protein
Function / homologyStimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / cyclic-di-GMP binding / activation of innate immune response / positive regulation of type I interferon production / Stimulator of interferon protein
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.1 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: 6nt5

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: 0.0233
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0233
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nt5
  • Surface level: 0.0233
  • 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_0502.map.gz (map file in CCP4 format, 37045 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
210 pix
0.84 Å/pix.
= 176.4 Å
210 pix
0.84 Å/pix.
= 176.4 Å
210 pix
0.84 Å/pix.
= 176.4 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:0.0233 (by author), 0.0233 (movie #1):
Minimum - Maximum-0.030996079 - 0.07230262
Average (Standard dev.)0.00025128003 (0.0032912088)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions210210210
Origin0.00.00.0
Limit209.0209.0209.0
Spacing210210210
CellA=B=C: 176.4 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/z210210210
origin x/y/z0.0000.0000.000
length x/y/z176.400176.400176.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS210210210
D min/max/mean-0.0310.0720.000

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Supplemental data

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Sample components

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Entire full-length human STING

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

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Component #1: protein, full-length human STING

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

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Component #2: protein, Stimulator of interferon protein

ProteinName: Stimulator of interferon protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 42.985379 kDa
SourceSpecies: Homo sapiens (human)
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: 5 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: 75479
3D reconstructionSoftware: RELION / Resolution: 4.1 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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