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- EMDB-0506: Cryo-EM structure of the complex between human TBK1 and chicken STING -

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Basic information

Entry
Database: EMDB / ID: 0506
TitleCryo-EM structure of the complex between human TBK1 and chicken STING
Map dataprimary map
Samplefull-length chicken STING and human TBK1:
STING / TBK1 / Serine/threonine-protein kinase TBK1 / Stimulator of interferon genes protein
Function / homologySTAT6-mediated induction of chemokines / Protein kinases ATP-binding region signature. / IRF3-mediated induction of type I IFN / Interleukin-37 signaling / Protein kinase domain / Protein kinase-like domain superfamily / TICAM1-dependent activation of IRF3/IRF7 / Protein kinase, ATP binding site / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily ...STAT6-mediated induction of chemokines / Protein kinases ATP-binding region signature. / IRF3-mediated induction of type I IFN / Interleukin-37 signaling / Protein kinase domain / Protein kinase-like domain superfamily / TICAM1-dependent activation of IRF3/IRF7 / Protein kinase, ATP binding site / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Protein kinase domain / Transmembrane protein 173 / Stimulator of interferon genes protein, C-terminal / TRAF3-dependent IRF activation pathway / IRF3 mediated activation of type 1 IFN / STING mediated induction of host immune responses / Regulation of innate immune responses to cytosolic DNA / Regulation of innate immune responses to cytosolic DNA / STAT6-mediated induction of chemokines / TRAF6 mediated IRF7 activation / Negative regulators of DDX58/IFIH1 signaling / Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon / Neutrophil degranulation / Protein kinase domain profile. / type I interferon production / dendritic cell proliferation / cyclic-GMP-AMP binding / interferon-beta production / positive regulation of xenophagy / cytoplasmic pattern recognition receptor signaling pathway in response to virus / cyclic-di-GMP binding / regulation of type I interferon production / positive regulation of interferon-beta biosynthetic process / positive regulation of type I interferon-mediated signaling pathway / cellular response to interferon-beta / positive regulation of interferon-alpha production / cellular response to exogenous dsRNA / positive regulation of defense response to virus by host / aggresome / negative regulation of type I interferon production / positive regulation of interferon-beta production / regulation of neuron death / positive regulation of macroautophagy / positive regulation of type I interferon production / cellular response to cytokine stimulus / TRIF-dependent toll-like receptor signaling pathway / response to virus / phosphoprotein binding / I-kappaB kinase/NF-kappaB signaling / peroxisome / regulation of inflammatory response / defense response to virus / peptidyl-threonine phosphorylation / positive regulation of peptidyl-serine phosphorylation / positive regulation of DNA-binding transcription factor activity / mitochondrial outer membrane / positive regulation of I-kappaB kinase/NF-kappaB signaling / nucleic acid binding / positive regulation of protein binding / protein phosphatase binding / endosome membrane / negative regulation of gene expression / non-specific serine/threonine protein kinase / peptidyl-serine phosphorylation / defense response to Gram-positive bacterium / protein kinase activity / inflammatory response / transcription factor binding / endoplasmic reticulum membrane / viral process / innate immune response / ubiquitin protein ligase binding / protein serine/threonine kinase activity / protein phosphorylation / protein kinase binding / Golgi apparatus / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / integral component of membrane / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm / Stimulator of interferon genes protein / Serine/threonine-protein kinase TBK1
Function and homology information
SourceGallus gallus (chicken) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsShang G / Zhang C / Chen ZJ / Bai X / Zhang X
CitationJournal: Nature / Year: 2019
Title: Structural basis of STING binding with and phosphorylation by TBK1.
Authors: Conggang Zhang / Guijun Shang / Xiang Gui / Xuewu Zhang / Xiao-Chen Bai / Zhijian J Chen
Validation ReportPDB-ID: 6nt9

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: 0.048
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.048
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6nt9
  • Surface level: 0.048
  • 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_0506.map.gz (map file in CCP4 format, 42593 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
220 pix
1.07 Å/pix.
= 235.4 Å
220 pix
1.07 Å/pix.
= 235.4 Å
220 pix
1.07 Å/pix.
= 235.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour Level:0.048 (by author), 0.048 (movie #1):
Minimum - Maximum-0.21360976 - 0.3472147
Average (Standard dev.)0.00058755354 (0.009017996)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions220220220
Origin0.00.00.0
Limit219.0219.0219.0
Spacing220220220
CellA=B=C: 235.40001 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z235.400235.400235.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.2140.3470.001

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Supplemental data

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Sample components

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Entire full-length chicken STING and human TBK1

EntireName: full-length chicken STING and human TBK1 / Number of components: 5

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Component #1: protein, full-length chicken STING and human TBK1

ProteinName: full-length chicken STING and human TBK1 / Recombinant expression: No

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Component #2: protein, STING

ProteinName: 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 #3: protein, TBK1

ProteinName: TBK1 / 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 #4: protein, Serine/threonine-protein kinase TBK1

ProteinName: Serine/threonine-protein kinase TBK1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 85.316695 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: 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: 48 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: 86276
3D reconstructionSoftware: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 4IM0
Output model

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