[English] 日本語
Yorodumi
- PDB-6a06: Structure of pSTING complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a06
TitleStructure of pSTING complex
ComponentsStimulator of interferon genes protein
KeywordsSIGNALING PROTEIN / pSTING
Function / homology
Function and homology information


proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / cGAS/STING signaling pathway / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / autophagosome / positive regulation of type I interferon production ...proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / cGAS/STING signaling pathway / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / autophagosome / positive regulation of type I interferon production / signaling adaptor activity / positive regulation of interferon-beta production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm / protein homodimerization activity / plasma membrane / cytoplasm
Similarity search - Function
Stimulator of interferon genes protein / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
cGAMP / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.792 Å
AuthorsYuan, Z.L. / Shang, G.J. / Cong, X.Y. / Gu, L.C.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Crystal structures of porcine STINGCBD-CDN complexes reveal the mechanism of ligand recognition and discrimination of STING proteins.
Authors: Cong, X. / Yuan, Z. / Du, Y. / Wu, B. / Lu, D. / Wu, X. / Zhang, Y. / Li, F. / Wei, B. / Li, J. / Wu, J. / Xu, S. / Wang, J. / Qi, J. / Shang, G. / Gu, L.
History
DepositionJun 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Stimulator of interferon genes protein
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7267
Polymers45,6682
Non-polymers1,0595
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-58 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.628, 63.311, 101.036
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Stimulator of interferon genes protein / / poSTING / Transmembrane protein 173


Mass: 22833.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TMEM173, STING / Production host: Escherichia coli (E. coli) / References: UniProt: B8XX90
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p] / Cyclic guanosine monophosphate–adenosine monophosphate


Mass: 674.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O13P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 29.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.5M Li2SO4, 0.1M NaOAC

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.792→50 Å / Num. obs: 30287 / % possible obs: 99.2 % / Redundancy: 7 % / Net I/σ(I): 47.45
Reflection shellResolution: 1.8→1.86 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.792→30.9 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 1999 6.6 %
Rwork0.1753 --
obs0.1784 30287 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.792→30.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 65 233 3239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063086
X-RAY DIFFRACTIONf_angle_d0.8574198
X-RAY DIFFRACTIONf_dihedral_angle_d18.5151825
X-RAY DIFFRACTIONf_chiral_restr0.054449
X-RAY DIFFRACTIONf_plane_restr0.005552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7924-1.83720.28291360.23641911X-RAY DIFFRACTION94
1.8372-1.88690.30521390.21211978X-RAY DIFFRACTION99
1.8869-1.94240.29731400.19311985X-RAY DIFFRACTION99
1.9424-2.0050.23221420.1762006X-RAY DIFFRACTION99
2.005-2.07670.25051410.18021998X-RAY DIFFRACTION99
2.0767-2.15980.20871430.18022016X-RAY DIFFRACTION99
2.1598-2.25810.2441430.17812017X-RAY DIFFRACTION100
2.2581-2.37710.23131410.18242009X-RAY DIFFRACTION100
2.3771-2.5260.23941430.19262037X-RAY DIFFRACTION100
2.526-2.72090.28931440.20492029X-RAY DIFFRACTION100
2.7209-2.99450.20561450.18642044X-RAY DIFFRACTION100
2.9945-3.42730.18831440.16432047X-RAY DIFFRACTION100
3.4273-4.31620.18421490.14632090X-RAY DIFFRACTION99
4.3162-30.90440.20951490.17192121X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 20.8836 Å / Origin y: 0.2549 Å / Origin z: -19.0052 Å
111213212223313233
T0.1704 Å20.0122 Å2-0.0111 Å2-0.1443 Å2-0.0283 Å2--0.1902 Å2
L0.6009 °2-0.0146 °2-0.0088 °2-0.2534 °20.1855 °2--1.742 °2
S0.0366 Å °0.0229 Å °-0.0157 Å °-0.0299 Å °-0.0021 Å °0.0406 Å °-0.0684 Å °-0.0694 Å °-0.0382 Å °
Refinement TLS groupSelection details: all

+
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