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- PDB-4lok: Crystal structure of mSting in complex with c[G(3',5')pA(3',5')p] -

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Basic information

Entry
Database: PDB / ID: 4lok
TitleCrystal structure of mSting in complex with c[G(3',5')pA(3',5')p]
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / innate immunity
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 / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / cGAS/STING 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 / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / cGAS/STING signaling pathway / positive regulation of type I interferon-mediated signaling pathway / reticulophagy / cellular response to exogenous dsRNA / cellular response to organic cyclic compound / protein complex oligomerization / positive regulation of type I interferon production / positive regulation of macroautophagy / autophagosome membrane / autophagosome assembly / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / activation of innate immune response / antiviral innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of interferon-beta production / autophagosome / Neutrophil degranulation / peroxisome / 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 / cytosol / cytoplasm
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
Chem-1YD / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsGao, P. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Structure-Function Analysis of STING Activation by c[G(2',5')pA(3',5')p] and Targeting by Antiviral DMXAA.
Authors: Gao, P. / Ascano, M. / Zillinger, T. / Wang, W. / Dai, P. / Serganov, A.A. / Gaffney, B.L. / Shuman, S. / Jones, R.A. / Deng, L. / Hartmann, G. / Barchet, W. / Tuschl, T. / Patel, D.J.
History
DepositionJul 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7653
Polymers43,0912
Non-polymers6741
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-19 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.385, 47.379, 156.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 21545.457 Da / Num. of mol.: 2 / Fragment: c-di-GMP-binding domain
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: Chemical ChemComp-1YD / 2-amino-9-[(2R,3R,3aR,5S,7aS,9R,10R,10aR,12R,14aS)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one


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


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M sodium formate, 20% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. all: 20709 / Num. obs: 20191 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.07→2.14 Å / % possible all: 94.3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→45.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.297 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1070 5 %RANDOM
Rwork0.177 ---
obs0.18 20191 97.1 %-
all-20709 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å20 Å2
2--2.67 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.07→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 45 139 3085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023066
X-RAY DIFFRACTIONr_bond_other_d0.0020.022884
X-RAY DIFFRACTIONr_angle_refined_deg1.8432.0124172
X-RAY DIFFRACTIONr_angle_other_deg1.2543.0116594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32423.462156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33415512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5551532
X-RAY DIFFRACTIONr_chiral_restr0.1220.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213470
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02748
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr12.14535950
X-RAY DIFFRACTIONr_sphericity_free10.454551
X-RAY DIFFRACTIONr_sphericity_bonded19.32255970
LS refinement shellResolution: 2.07→2.12 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 62 -
Rwork0.236 1361 -
obs--90.23 %

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