[English] 日本語
Yorodumi
- EMDB-35503: Cryo-EM structure of Stimulator of interferon genes -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35503
TitleCryo-EM structure of Stimulator of interferon genes
Map data
Sample
  • Complex: fiber of adaptor protein
    • Protein or peptide: Stimulator of interferon genes protein,Immune protein Tsi3
Keywordsadaptor protein / IMMUNE SYSTEM
Function / homology
Function and homology information


STING mediated induction of host immune responses / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / cGAS/STING signaling pathway / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production ...STING mediated induction of host immune responses / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / cGAS/STING signaling pathway / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / autophagosome / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / positive regulation of interferon-beta production / Neutrophil degranulation / protein complex oligomerization / cytoplasmic vesicle / defense response to virus / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm / protein homodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
: / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Stimulator of interferon genes protein / Immune protein Tsi3
Similarity search - Component
Biological speciesGallus gallus (chicken) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLu DF / Shang GJ
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2301400 China
CitationJournal: Mol Cell / Year: 2023
Title: The mechanism of STING autoinhibition and activation.
Authors: Sheng Liu / Bo Yang / Yingxiang Hou / Kaige Cui / Xiaozhu Yang / Xiaoxiong Li / Lianwan Chen / Shichao Liu / Zhichao Zhang / Yuanyuan Jia / Yufeng Xie / Ying Xue / Xiaomei Li / Bingxue Yan / ...Authors: Sheng Liu / Bo Yang / Yingxiang Hou / Kaige Cui / Xiaozhu Yang / Xiaoxiong Li / Lianwan Chen / Shichao Liu / Zhichao Zhang / Yuanyuan Jia / Yufeng Xie / Ying Xue / Xiaomei Li / Bingxue Yan / Changxin Wu / Wen Deng / Jianxun Qi / Defen Lu / George F Gao / Peiyi Wang / Guijun Shang /
Abstract: 2',3'-cGAMP, produced by the DNA sensor cGAS, activates stimulator of interferon genes (STING) and triggers immune response during infection. Tremendous effort has been placed on unraveling the ...2',3'-cGAMP, produced by the DNA sensor cGAS, activates stimulator of interferon genes (STING) and triggers immune response during infection. Tremendous effort has been placed on unraveling the mechanism of STING activation. However, little is known about STING inhibition. Here, we found that apo-STING exhibits a bilayer with head-to-head as well as side-by-side packing, mediated by its ligand-binding domain (LBD). This type of assembly holds two endoplasmic reticulum (ER) membranes together not only to prevent STING ER exit but also to eliminate the recruitment of TBK1, representing the autoinhibited state of STING. Additionally, we obtained the filament structure of the STING/2',3'-cGAMP complex, which adopts a bent monolayer assembly mediated by LBD and transmembrane domain (TMD). The active, curved STING polymer could deform ER membrane to support its ER exit and anterograde transportation. Our data together provide a panoramic vision regarding STING autoinhibition and activation, which adds substantially to current understanding of the cGAS-STING pathway.
History
DepositionFeb 28, 2023-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_35503.png

Downloads & links

-
Map

FileDownload / File: emd_35503.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.095 Å
Density
Contour LevelBy AUTHOR: 0.339
Minimum - Maximum-2.9866452 - 4.323909
Average (Standard dev.)0.020000843 (±0.109440304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_35503_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35503_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : fiber of adaptor protein

EntireName: fiber of adaptor protein
Components
  • Complex: fiber of adaptor protein
    • Protein or peptide: Stimulator of interferon genes protein,Immune protein Tsi3

-
Supramolecule #1: fiber of adaptor protein

SupramoleculeName: fiber of adaptor protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Gallus gallus (chicken)

-
Macromolecule #1: Stimulator of interferon genes protein,Immune protein Tsi3

MacromoleculeName: Stimulator of interferon genes protein,Immune protein Tsi3
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Molecular weightTheoretical: 55.282332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPQDPSTRSS PARLLIPEPR AGRARHAACV LLAVCFVVLF LSGEPLAPIT RRVCTQLAAL QLGVLLKGCC CLAEEIFHLH SRHHGSLWQ VLCSCFPPRW HLALLLVGGS AYLDPPEDNG HSPRLALTLS CLCQLLVLAL GLQKLSAVEV SELTESSKKN V AHGLAWSY ...String:
MPQDPSTRSS PARLLIPEPR AGRARHAACV LLAVCFVVLF LSGEPLAPIT RRVCTQLAAL QLGVLLKGCC CLAEEIFHLH SRHHGSLWQ VLCSCFPPRW HLALLLVGGS AYLDPPEDNG HSPRLALTLS CLCQLLVLAL GLQKLSAVEV SELTESSKKN V AHGLAWSY YIGYLKVVLP RLKECMEEIS RTNPMLRAHR DTWKLHILVP LGCDIWDDLE KADSNIQYLA DLPETILTRA GI KRRVYKH SLYVIRDKDN KLRPCVLEFA SPLQTLCAMS QDDCAAFSRE QRLEQARLFY RSLRDILGSS KECAGLYRLI AYE EPAEPE SHFLSGLILW HLQQQQREEY MVLEVLFQGP VDFDKTLTHP NGLVVERPVG FDARRSAEGF RFDEGGKLRN PRQL EVQRQ DAPPPPDLAS RRLGDGEARY KVEEDDGGSA GSEYRLWAAK PAGARWIVVS ASEQSEDGEP TFALAWALLE RARLQ SSHH HHHHHH

UniProtKB: Stimulator of interferon genes protein, Immune protein Tsi3

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.5
Details: 20mM HEPES, 150mM NaCl, 1mM TCEP, 0.03% DDM/CHS(5:1)
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6nt6

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1057869

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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