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- PDB-6xnp: Crystal Structure of Human STING CTD complex with SR-717 -

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Basic information

Entry
Database: PDB / ID: 6xnp
TitleCrystal Structure of Human STING CTD complex with SR-717
ComponentsStimulator of interferon protein
KeywordsIMMUNE SYSTEM / Agonist / Complex / Closed conformation / Immunity
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / proton channel activity / 2',3'-cyclic GMP-AMP binding / STING mediated induction of host immune responses / cyclic-di-GMP binding / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / proton channel activity / 2',3'-cyclic GMP-AMP binding / STING mediated induction of host immune responses / cyclic-di-GMP binding / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / reticulophagy / pattern recognition receptor signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / 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 / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / positive regulation of interferon-beta production / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / cytoplasmic vesicle membrane / positive regulation of DNA-binding transcription factor activity / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein complex oligomerization / regulation of inflammatory response / cytoplasmic vesicle / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / 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 / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 protein
B: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1377
Polymers43,2012
Non-polymers9375
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-18 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.487, 77.627, 135.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Stimulator of interferon protein


Mass: 21600.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING, LOC340061, hCG_1782396 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R3XZB7, UniProt: Q86WV6*PLUS
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 296 K / Method: batch mode / Details: PEG8000, calcium acetate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 35421 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Χ2: 0.974 / Net I/σ(I): 7.7 / Num. measured all: 228421
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.836.40.34334750.9250.1470.3741.216100
1.83-1.916.70.2534530.970.1050.2721.096100
1.91-1.996.50.17834910.9830.0760.1941.003100
1.99-2.16.20.13235120.9890.0570.1441.028100
2.1-2.236.70.10335130.9940.0430.1111.012100
2.23-2.46.50.08234900.9950.0350.0890.99999.9
2.4-2.646.30.06735250.9970.0290.0730.954100
2.64-3.036.60.05335790.9970.0220.0580.887100
3.03-3.816.40.03835770.9990.0160.0410.816100
3.81-506.10.03238060.9990.0140.0350.741100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EMT

4emt


Resolution: 1.77→39.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.289 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 1774 5 %RANDOM
Rwork0.1604 ---
obs0.1625 33577 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.83 Å2 / Biso mean: 20.01 Å2 / Biso min: 8.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2---0.17 Å20 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 1.77→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 66 353 3323
Biso mean--19.1 31.99 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133205
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172876
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.6684365
X-RAY DIFFRACTIONr_angle_other_deg1.4861.586672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8395395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94321.287202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15815540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5621534
X-RAY DIFFRACTIONr_chiral_restr0.0870.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023729
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02727
LS refinement shellResolution: 1.77→1.815 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.22 129 -
Rwork0.187 2347 -
obs--97.25 %

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