6NT9

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  
    6NT9

  • 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 1 . Cyclic GMP-AMP synthase (cGAS) is a sensor of cytoplasmic DNA that activates the type-I interferon pathway 2 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase TBK1A,
C [auth B]
742Homo sapiensMutation(s): 1 
Gene Names: TBK1NAK
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHD2 (Homo sapiens)
Explore Q9UHD2 
Go to UniProtKB:  Q9UHD2
PHAROS:  Q9UHD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHD2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Stimulator of interferon genes proteinB [auth C],
D
392Gallus gallusMutation(s): 0 
Gene Names: TMEM173STING1STING
Membrane Entity: Yes 
UniProt
Find proteins for E1C7U0 (Gallus gallus)
Explore E1C7U0 
Go to UniProtKB:  E1C7U0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C7U0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM088197
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM130289
Howard Hughes Medical Institute (HHMI)United States--
Welch FoundationUnited StatesI-1389
Welch FoundationUnited StatesI-1702
Welch FoundationUnited StatesI-1944

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-18
    Changes: Other