[English] 日本語
Yorodumi
- PDB-6cff: Stimulator of Interferon Genes Human -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cff
TitleStimulator of Interferon Genes Human
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / human STING / complex / cyclic-di-AMP / TMEM173 / wild type / 230G/232R
Function / homology
Function and homology information


STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / proton channel activity / reticulophagy / pattern recognition receptor signaling pathway ...STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / proton channel activity / reticulophagy / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway / cellular response to exogenous dsRNA / Dengue virus activates/modulates innate and adaptive immune responses / cytoplasmic pattern recognition receptor signaling pathway / protein complex oligomerization / positive regulation of macroautophagy / autophagosome membrane / autophagosome assembly / positive regulation of defense response to virus by host / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / signaling adaptor activity / positive regulation of interferon-beta production / autophagosome / cytoplasmic vesicle membrane / secretory granule membrane / Regulation of innate immune responses to cytosolic DNA / antiviral innate immune response / protein serine/threonine kinase binding / SARS-CoV-1 activates/modulates innate immune responses / peroxisome / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / transcription coactivator activity / endosome / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / protein kinase binding / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Stimulator of interferon genes protein / : / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsFernandez, D. / Li, L. / Ergun, S.L.
Citation
Journal: Cell / Year: 2019
Title: STING Polymer Structure Reveals Mechanisms for Activation, Hyperactivation, and Inhibition.
Authors: Ergun, S.L. / Fernandez, D. / Weiss, T.M. / Li, L.
#1: Journal: Biorxiv / Year: 2019
Title: STING polymer structure reveals mechanisms for activation, hyperactivation, and inhibition
Authors: Ergun, S.L. / Fernandez, D. / Weiss, T.M. / Li, L.
History
DepositionFeb 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Aug 7, 2019Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_id_ISSN ..._chem_comp.name / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7822
Polymers27,1241
Non-polymers6581
Water1,20767
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5644
Polymers54,2472
Non-polymers1,3172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3950 Å2
ΔGint-15 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.930, 110.930, 36.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Stimulator of interferon genes protein / hSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / hMITA / ...hSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / hMITA / Transmembrane protein 173


Mass: 27123.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM173, ERIS, MITA, STING / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WV6
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: Sodium citrate tribasic, PEG 3350, pH 8.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2017
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.396→40 Å / Num. obs: 8466 / % possible obs: 97.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.048 / Rrim(I) all: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 2.396→2.457 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1216 / CC1/2: 0.794 / Rpim(I) all: 0.33 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.396→20.09 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.972 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.263 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24918 885 9.8 %RANDOM
Rwork0.1927 ---
obs0.19833 7962 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å2-0 Å2-0 Å2
2--0.94 Å2-0 Å2
3----1.88 Å2
Refinement stepCycle: 1 / Resolution: 2.396→20.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 22 67 1440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191400
X-RAY DIFFRACTIONr_bond_other_d0.0020.021278
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9961898
X-RAY DIFFRACTIONr_angle_other_deg1.0532956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4123.7572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.53115238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4711514
X-RAY DIFFRACTIONr_chiral_restr0.1030.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.74.97669
X-RAY DIFFRACTIONr_mcbond_other3.6994.969668
X-RAY DIFFRACTIONr_mcangle_it5.5927.43831
X-RAY DIFFRACTIONr_mcangle_other5.5897.432832
X-RAY DIFFRACTIONr_scbond_it4.4335.503731
X-RAY DIFFRACTIONr_scbond_other4.4335.503731
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9428.0531068
X-RAY DIFFRACTIONr_long_range_B_refined9.50657.9681537
X-RAY DIFFRACTIONr_long_range_B_other9.51157.931535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.396→2.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 63 -
Rwork0.282 581 -
obs--98.77 %

+
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