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- PDB-4kc0: mSTING -

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Basic information

Entry
Database: PDB / ID: 4kc0
TitlemSTING
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / mouse STING
Function / homology
Function and homology information


STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / Regulation of innate immune responses to cytosolic DNA / STING complex / protein localization to endoplasmic reticulum / proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of type I interferon-mediated signaling pathway ...STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / Regulation of innate immune responses to cytosolic DNA / STING complex / protein localization to endoplasmic reticulum / proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / reticulophagy / cellular response to exogenous dsRNA / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / cellular response to organic cyclic compound / autophagosome assembly / autophagosome / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / activation of innate immune response / positive regulation of interferon-beta production / Neutrophil degranulation / endoplasmic reticulum-Golgi intermediate compartment membrane / peroxisome / protein complex oligomerization / regulation of inflammatory response / regulation of gene expression / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / lysosomal membrane / Golgi membrane / innate immune response / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Stimulator of interferon genes protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChin, K.H. / Su, Y.C. / Tu, J.L. / Chou, S.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Novel c-di-GMP recognition modes of the mouse innate immune adaptor protein STING
Authors: Chin, K.H. / Tu, Z.L. / Su, Y.C. / Yu, Y.J. / Chen, H.C. / Lo, Y.C. / Chen, C.P. / Barber, G.N. / Chuah, M.L. / Liang, Z.X. / Chou, S.H.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 29, 2013ID: 4G3L
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,1822
Polymers47,1822
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-13 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.493, 78.493, 50.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 23590.846 Da / Num. of mol.: 2
Fragment: c-di-GMP-binding domain (CBD), UNP residues 138-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tmem173, Eris Mita, Mpys, Sting / Production host: Escherichia coli (E. coli) / References: UniProt: Q3TBT3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Tris 8.0, 20% PEG 3350 MME, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97898 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2011
RadiationMonochromator: Se SAD / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 17389 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→25.693 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.798 / SU ML: 0.27 / σ(F): 0.21 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 1716 9.87 %
Rwork0.1939 --
obs0.2004 17389 98.45 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.084 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 148.35 Å2 / Biso mean: 47.461 Å2 / Biso min: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.0843 Å20 Å2-0 Å2
2--4.0843 Å2-0 Å2
3----8.1687 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 0 65 2970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082957
X-RAY DIFFRACTIONf_angle_d1.1424000
X-RAY DIFFRACTIONf_dihedral_angle_d14.551134
X-RAY DIFFRACTIONf_chiral_restr0.078439
X-RAY DIFFRACTIONf_plane_restr0.004532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1982-2.26290.29411440.2472124895
2.2629-2.33590.31381440.2169126995
2.3359-2.41930.27881440.2084126598
2.4193-2.51610.30261480.2021132598
2.5161-2.63050.30321340.1966131498
2.6305-2.7690.29541380.2087131099
2.769-2.94230.30971500.1885130599
2.9423-3.16910.34411290.20111345100
3.1691-3.48730.23461420.20191327100
3.4873-3.99030.21161520.16841309100
3.9903-5.02120.21851500.16071330100
5.0212-25.69460.2431410.21781326100
Refinement TLS params.Method: refined / Origin x: -15.4904 Å / Origin y: -18.4098 Å / Origin z: -7.7707 Å
111213212223313233
T0.2188 Å2-0.0193 Å2-0.022 Å2-0.2577 Å2-0.0125 Å2--0.2269 Å2
L1.7034 °20.601 °2-0.8201 °2-1.0157 °2-0.4055 °2--1.4085 °2
S-0.0828 Å °-0.0433 Å °-0.1422 Å °-0.0464 Å °0.0116 Å °-0.0894 Å °0.1952 Å °0.1152 Å °0.0495 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA152 - 336
2X-RAY DIFFRACTION1allB154 - 335

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