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- PDB-4lol: Crystal structure of mSting in complex with DMXAA -

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Basic information

Entry
Database: PDB / ID: 4lol
TitleCrystal structure of mSting in complex with DMXAA
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 / STING complex / Regulation of innate immune responses to cytosolic DNA / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of type I interferon-mediated signaling pathway / proton channel activity ...STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / STING complex / Regulation of innate immune responses to cytosolic DNA / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of type I interferon-mediated signaling pathway / proton channel activity / cGAS/STING signaling pathway / regulation of metabolic process / reticulophagy / cellular response to exogenous dsRNA / protein complex oligomerization / positive regulation of macroautophagy / autophagosome membrane / autophagosome assembly / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / antiviral innate immune response / Neutrophil degranulation / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / autophagosome / positive regulation of interferon-beta production / peroxisome / regulation of gene expression / regulation of inflammatory response / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / ciliary basal body / endosome / Golgi membrane / lysosomal 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 / : / : / STING transmembrane domain / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / 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 / 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
(5,6-dimethyl-9-oxo-9H-xanthen-4-yl)acetic acid / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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 21, 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)43,6554
Polymers43,0912
Non-polymers5652
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-14 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.376, 108.376, 101.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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-1YE / (5,6-dimethyl-9-oxo-9H-xanthen-4-yl)acetic acid


Mass: 282.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.6 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. all: 15852 / Num. obs: 15773 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.43→2.57 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.7.0032refinement
RAPDdata reduction
RAPDdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→44.58 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20851 844 5.1 %RANDOM
Rwork0.18267 ---
obs0.18398 15773 99.39 %-
all-15852 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.849 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.35 Å20 Å2
2--0.35 Å2-0 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.43→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2838 0 42 32 2912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192935
X-RAY DIFFRACTIONr_bond_other_d00.022812
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9873974
X-RAY DIFFRACTIONr_angle_other_deg3.5373.0036410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9825347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58723.311151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.99715499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4881532
X-RAY DIFFRACTIONr_chiral_restr0.0950.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213352
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02720
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_it12.0046.0141406
X-RAY DIFFRACTIONr_mcbond_other11.9666.0111405
X-RAY DIFFRACTIONr_mcangle_it13.7619.0031747
X-RAY DIFFRACTIONr_mcangle_other13.949.1291782
X-RAY DIFFRACTIONr_scbond_it12.3676.1831529
X-RAY DIFFRACTIONr_scbond_other12.6066.3091542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.7629.2952251
X-RAY DIFFRACTIONr_long_range_B_refined14.34947.8283425
X-RAY DIFFRACTIONr_long_range_B_other14.34847.8343421
X-RAY DIFFRACTIONr_rigid_bond_restr14.64835747
X-RAY DIFFRACTIONr_sphericity_free10.46524
X-RAY DIFFRACTIONr_sphericity_bonded25.04455707
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 66 -
Rwork0.309 1164 -
obs--99.92 %

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