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- PDB-6xnn: Crystal Structure of Mouse STING CTD complex with SR-717. -

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Basic information

Entry
Database: PDB / ID: 6xnn
TitleCrystal Structure of Mouse STING CTD complex with SR-717.
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / Agonist / Complex / Closed Conformation / 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 / 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
: / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173
Similarity search - Domain/homology
Chem-V67 / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
AuthorsChin, E.N. / Yu, C. / Wolan, D.W. / Petrassi, H.M. / Lairson, L.L.
CitationJournal: Science / Year: 2020
Title: Antitumor activity of a systemic STING-activating non-nucleotide cGAMP mimetic.
Authors: Chin, E.N. / Yu, C. / Vartabedian, V.F. / Jia, Y. / Kumar, M. / Gamo, A.M. / Vernier, W. / Ali, S.H. / Kissai, M. / Lazar, D.C. / Nguyen, N. / Pereira, L.E. / Benish, B. / Woods, A.K. / ...Authors: Chin, E.N. / Yu, C. / Vartabedian, V.F. / Jia, Y. / Kumar, M. / Gamo, A.M. / Vernier, W. / Ali, S.H. / Kissai, M. / Lazar, D.C. / Nguyen, N. / Pereira, L.E. / Benish, B. / Woods, A.K. / Joseph, S.B. / Chu, A. / Johnson, K.A. / Sander, P.N. / Martinez-Pena, F. / Hampton, E.N. / Young, T.S. / Wolan, D.W. / Chatterjee, A.K. / Schultz, P.G. / Petrassi, H.M. / Teijaro, J.R. / Lairson, L.L.
History
DepositionJul 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6074
Polymers42,9172
Non-polymers6912
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-18 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.680, 65.680, 172.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: 21458.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sting1, Eris, Mita, Mpys, Tmem173 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3TBT3
#2: Chemical ChemComp-V67 / 4,5-difluoro-2-{[6-(1H-imidazol-1-yl)pyridazine-3-carbonyl]amino}benzoic acid


Mass: 345.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H9F2N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 297 K / Method: batch mode / Details: PEG3350, calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.49→46.49 Å / Num. obs: 13976 / % possible obs: 99.6 % / Redundancy: 8.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.028 / Rrim(I) all: 0.082 / Net I/σ(I): 20.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.49-2.598.60.6791284414950.8690.2390.7223.497.3
8.97-46.446.60.02823743600.9990.0110.03151.997.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOJ

4loj


Resolution: 2.49→46.44 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / SU B: 23.216 / SU ML: 0.287 / SU R Cruickshank DPI: 1.1582 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.158 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 674 4.8 %RANDOM
Rwork0.2221 ---
obs0.2247 13267 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.35 Å2 / Biso mean: 54.169 Å2 / Biso min: 21.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å2-0 Å2-0 Å2
2--2.03 Å2-0 Å2
3----4.06 Å2
Refinement stepCycle: final / Resolution: 2.49→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 100 129 3132
Biso mean--28.9 49.54 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133067
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172760
X-RAY DIFFRACTIONr_angle_refined_deg1.471.6914156
X-RAY DIFFRACTIONr_angle_other_deg1.1771.5846375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7355359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89821.217189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95115512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6711532
X-RAY DIFFRACTIONr_chiral_restr0.0640.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02691
LS refinement shellResolution: 2.49→2.551 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.393 51 -
Rwork0.276 906 -
obs--95.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8479-0.26720.2411.2454-0.82570.65570.03020.0733-0.22650.2901-0.00510.2222-0.27770.0576-0.02510.2127-0.04-0.02180.0310.02270.3153-20.38287.2621-5.1425
21.3906-1.1231.28271.3399-1.4791.85830.00680.62750.23710.2462-0.5821-0.227-0.37660.76520.57530.1989-0.1201-0.18970.37040.23730.44391.34318.8715-19.5312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A155 - 334
2X-RAY DIFFRACTION2B155 - 335

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