[English] 日本語
Yorodumi
- PDB-6nt9: Cryo-EM structure of the complex between human TBK1 and chicken STING -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6nt9
TitleCryo-EM structure of the complex between human TBK1 and chicken STING
Components
  • Serine/threonine-protein kinase TBK1
  • Stimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / ER / kinase / adaptor
Function / homologyTANK binding kinase 1 ubiquitin-like domain / Neutrophil degranulation / Protein kinase domain / Protein kinase-like domain superfamily / 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 / Protein kinases ATP-binding region signature. ...TANK binding kinase 1 ubiquitin-like domain / Neutrophil degranulation / Protein kinase domain / Protein kinase-like domain superfamily / 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 / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / STING mediated induction of host immune responses / Regulation of innate immune responses to cytosolic DNA / STAT6-mediated induction of chemokines / Stimulator of interferon genes protein, C-terminal / TANK-binding kinase 1 coiled-coil domain 1 / Regulation of innate immune responses to cytosolic DNA / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / Interleukin-37 signaling / Negative regulators of DDX58/IFIH1 signaling / TRAF6 mediated IRF7 activation / IRF3 mediated activation of type 1 IFN / Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon / TICAM1-dependent activation of IRF3/IRF7 / TRAF3-dependent IRF activation pathway / type I interferon production / dendritic cell proliferation / cyclic-GMP-AMP binding / interferon-beta production / positive regulation of xenophagy / cyclic-di-GMP binding / cytoplasmic pattern recognition receptor signaling pathway in response to virus / 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
Specimen sourceHomo sapiens (human)
Gallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsShang, G. / Zhang, C. / Chen, Z.J. / Bai, X. / Zhang, X.
Funding supportUnited States , 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM088197United States
National Institutes of Health/National Institute of General Medical SciencesR35GM130289United States
Howard Hughes Medical InstituteUnited States
Welch FoundationI-1389United States
Welch FoundationI-1702United States
Welch FoundationI-1944United States
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jan 28, 2019 / Release: Mar 6, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 6, 2019Structure modelrepositoryInitial release
1.1Mar 20, 2019Structure modelData collection / Database referencescitation / citation_author_citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0506
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase TBK1
C: Stimulator of interferon genes protein
B: Serine/threonine-protein kinase TBK1
D: Stimulator of interferon genes protein


Theoretical massNumber of molelcules
Total (without water)259,0484
Polyers259,0484
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein/peptide Serine/threonine-protein kinase TBK1 / NF-kappa-B-activating kinase / T2K / TANK-binding kinase 1


Mass: 85316.695 Da / Num. of mol.: 2 / Mutation: D135N / Source: (gene. exp.) Homo sapiens (human) / Gene: TBK1, NAK / Production host: Homo sapiens (human)
References: UniProt: Q9UHD2, non-specific serine/threonine protein kinase
#2: Protein/peptide Stimulator of interferon genes protein /


Mass: 44207.070 Da / Num. of mol.: 2 / Source: (gene. exp.) Gallus gallus (chicken) / Gene: TMEM173Stimulator of interferon genes / Production host: Homo sapiens (human) / References: UniProt: A0A1D5P7Q9

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1full-length chicken STING and human TBK1COMPLEX1, 20RECOMBINANT
2STINGCOMPLEX21RECOMBINANT
3TBK1COMPLEX11RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129031Gallus gallus (chicken)
239606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDCellNcbi tax IDOrganism
12HEK293 GnTI-9606Homo sapiens (human)
23HEK293 GnTI-9606Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 30

-
Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 86276 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL
Atomic model buildingPDB-ID: 4IM0

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more