6NT9

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of STING binding with and phosphorylation by TBK1.

Zhang, C.Shang, G.Gui, X.Zhang, X.Bai, X.C.Chen, Z.J.

(2019) Nature 567: 394-398

  • DOI: 10.1038/s41586-019-1000-2

  • PubMed Abstract: 
  • The invasion of mammalian cytoplasm by microbial DNA from infectious pathogens or by self DNA from the nucleus or mitochondria represents a danger signal that alerts the host immune system <sup>1 </sup>. Cyclic GMP-AMP synthase (cGAS) is a sensor of ...

    The invasion of mammalian cytoplasm by microbial DNA from infectious pathogens or by self DNA from the nucleus or mitochondria represents a danger signal that alerts the host immune system 1 . Cyclic GMP-AMP synthase (cGAS) is a sensor of cytoplasmic DNA that activates the type-I interferon pathway 2 . On binding to DNA, cGAS is activated to catalyse the synthesis of cyclic GMP-AMP (cGAMP) from GTP and ATP 3 . cGAMP functions as a second messenger that binds to and activates stimulator of interferon genes (STING) 3-9 . STING then recruits and activates tank-binding kinase 1 (TBK1), which phosphorylates STING and the transcription factor IRF3 to induce type-I interferons and other cytokines 10,11 . However, how cGAMP-bound STING activates TBK1 and IRF3 is not understood. Here we present the cryo-electron microscopy structure of human TBK1 in complex with cGAMP-bound, full-length chicken STING. The structure reveals that the C-terminal tail of STING adopts a β-strand-like conformation and inserts into a groove between the kinase domain of one TBK1 subunit and the scaffold and dimerization domain of the second subunit in the TBK1 dimer. In this binding mode, the phosphorylation site Ser366 in the STING tail cannot reach the kinase-domain active site of bound TBK1, which suggests that STING phosphorylation by TBK1 requires the oligomerization of both proteins. Mutational analyses validate the interaction mode between TBK1 and STING and support a model in which high-order oligomerization of STING and TBK1, induced by cGAMP, leads to STING phosphorylation by TBK1.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xiaochen.Bai@UTSouthwestern.edu.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xiaochen.Bai@UTSouthwestern.edu.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xuewu.Zhang@UTSouthwestern.edu.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. Xuewu.Zhang@UTSouthwestern.edu.,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Zhijian.Chen@UTSouthwestern.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase TBK1
A, B
742Homo sapiensMutation(s): 1 
Gene Names: TBK1 (NAK)
EC: 2.7.11.1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Host-Defense Proteins
Protein: 
STING (aka TMEM173, MITA, ERIS, or MPHYS) apo state
Find proteins for Q9UHD2 (Homo sapiens)
Go to Gene View: TBK1
Go to UniProtKB:  Q9UHD2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Stimulator of interferon genes protein
C, D
392Gallus gallusMutation(s): 0 
Gene Names: TMEM173 (STING)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Host-Defense Proteins
Protein: 
STING (aka TMEM173, MITA, ERIS, or MPHYS) apo state
Find proteins for E1C7U0 (Gallus gallus)
Go to Gene View: TMEM173
Go to UniProtKB:  E1C7U0
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM088197
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35GM130289
Howard Hughes Medical InstituteUnited States--
Welch FoundationUnited StatesI-1389
Welch FoundationUnited StatesI-1702
Welch FoundationUnited StatesI-1944

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-03-20
    Type: Data collection, Database references
  • Version 1.2: 2019-04-03
    Type: Data collection, Database references