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- PDB-8sti: human STING with agonist XMT-1616 -

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Basic information

Entry
Database: PDB / ID: 8sti
Titlehuman STING with agonist XMT-1616
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM/AGONIST / Agonist / STING / IMMUNE SYSTEM / IMMUNE SYSTEM-AGONIST complex
Function / homology
Function and homology information


STING complex / STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway ...STING complex / STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor 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 / Regulation of innate immune responses to cytosolic DNA / secretory granule membrane / positive regulation of DNA-binding transcription factor activity / cytoplasmic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / peroxisome / regulation of inflammatory response / 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-WX8 / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.72 Å
AuthorsDuvall, J.R. / Bukhalid, R.A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery and Optimization of a STING Agonist Platform for Application in Antibody Drug Conjugates.
Authors: Duvall, J.R. / Thomas, J.D. / Bukhalid, R.A. / Catcott, K.C. / Bentley, K.W. / Collins, S.D. / Eitas, T. / Jones, B.D. / Kelleher, E.W. / Lancaster, K. / Protopopova, M. / Ray, S.S. / Ter- ...Authors: Duvall, J.R. / Thomas, J.D. / Bukhalid, R.A. / Catcott, K.C. / Bentley, K.W. / Collins, S.D. / Eitas, T. / Jones, B.D. / Kelleher, E.W. / Lancaster, K. / Protopopova, M. / Ray, S.S. / Ter-Ovanesyan, E. / Xu, L. / Yang, L. / Zurita, J. / Damelin, M. / Toader, D. / Lowinger, T.B.
History
DepositionMay 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 16, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2432
Polymers21,4891
Non-polymers7541
Water1,54986
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4864
Polymers42,9782
Non-polymers1,5082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)111.519, 111.519, 35.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

21A-568-

HOH

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Components

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


Mass: 21489.160 Da / Num. of mol.: 1 / Fragment: Cyclic dinucleotide-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING1, ERIS, MITA, STING, TMEM173 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WV6
#2: Chemical ChemComp-WX8 / 3-[(2E)-4-{5-carbamoyl-2-[(4-ethyl-2-methyl-1,3-oxazole-5-carbonyl)amino]-7-(3-hydroxypropoxy)-1H-benzimidazol-1-yl}but-2-en-1-yl]-2-[(4-ethyl-2-methyl-1,3-oxazole-5-carbonyl)amino]-3H-imidazo[4,5-b]pyridine-6-carboxamide


Mass: 753.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H39N11O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350; ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→78.86 Å / Num. obs: 24490 / % possible obs: 99.6 % / Redundancy: 15.8 % / CC1/2: 1 / Net I/σ(I): 24
Reflection shellResolution: 1.72→78.86 Å / Num. unique obs: 24490 / CC1/2: 1

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Jan 31data reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
REFMAC5.8.0155refinement
REFMACphasing
RefinementMethod to determine structure: MIR / Resolution: 1.72→78.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.52 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25697 2354 10 %RANDOM
Rwork0.20728 ---
obs0.21227 21224 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.178 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0 Å2
2--0.41 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.72→78.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 55 86 1544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191556
X-RAY DIFFRACTIONr_bond_other_d0.0030.021435
X-RAY DIFFRACTIONr_angle_refined_deg1.5212.0092126
X-RAY DIFFRACTIONr_angle_other_deg1.21533270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00523.53782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41115.061246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5711513
X-RAY DIFFRACTIONr_chiral_restr0.090.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211850
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02377
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_it3.1863.772752
X-RAY DIFFRACTIONr_mcbond_other3.1793.762751
X-RAY DIFFRACTIONr_mcangle_it4.9656.292947
X-RAY DIFFRACTIONr_mcangle_other4.9666.305948
X-RAY DIFFRACTIONr_scbond_it3.5374.021804
X-RAY DIFFRACTIONr_scbond_other3.5354.022805
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3356.6311180
X-RAY DIFFRACTIONr_long_range_B_refined8.29331.8321631
X-RAY DIFFRACTIONr_long_range_B_other8.24531.51620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.721→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 168 -
Rwork0.32 1594 -
obs--100 %
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)
16.10410.773-0.28261.50960.10371.96770.0317-0.2198-0.01860.054-0.06120.30490.0771-0.3340.02960.0269-0.01540.01250.0686-0.00630.06718.515-30.2649.476
27.4855-0.21230.3981.8771-2.00972.1876-0.03740.08960.23220.23880.0058-0.0415-0.31640.02740.03160.1705-0.02710.02230.07790.00340.12337.12-15.3912.452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A153 - 225
2X-RAY DIFFRACTION1A243 - 338
3X-RAY DIFFRACTION2A226 - 242

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