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- PDB-8t5k: Crystal structure of STING CTD in complex with BDW-OH -

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Basic information

Entry
Database: PDB / ID: 8t5k
TitleCrystal structure of STING CTD in complex with BDW-OH
ComponentsStimulator of interferon genes protein
KeywordsANTIVIRAL PROTEIN / Mediator of IRF3 activation / Stimulator of interferon genes protein
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / 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 / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / 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 / activation of innate immune response / Regulation of innate immune responses to cytosolic DNA / 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 / 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-YGI / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLi, Y. / Li, P. / Sun, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145287 United States
CitationJournal: Biorxiv / Year: 2023
Title: Structural and Biological Evaluations of a Non-Nucleoside STING Agonist Specific for Human STING A230 Variants.
Authors: Tang, Z. / Zhao, J. / Li, Y. / Tomer, S. / Selvaraju, M. / Tien, N. / Sun, D. / Johnson, D.K. / Zhen, A. / Li, P. / Wang, J.
History
DepositionJun 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8522
Polymers21,5571
Non-polymers2941
Water1,54986
1
B: Stimulator of interferon genes protein
hetero molecules

B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7034
Polymers43,1142
Non-polymers5892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4230 Å2
ΔGint-12 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.340, 77.110, 36.160
Angle α, β, γ (deg.)90.000, 97.960, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-536-

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: 21557.230 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 154-341)
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-YGI / {[(4S)-8,9-dimethylthieno[3,2-e][1,2,4]triazolo[4,3-c]pyrimidin-3-yl]sulfanyl}acetic acid


Mass: 294.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N4O2S2 / 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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→58.41 Å / Num. obs: 17718 / % possible obs: 98.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.66 Å2 / CC1/2: 0.929 / Net I/σ(I): 9.8
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 1112 / CC1/2: 0.376

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EMT

4emt


Resolution: 1.95→58.41 Å / SU ML: 0.2642 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.316
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2298 853 4.82 %
Rwork0.1977 16852 -
obs0.1994 17705 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.16 Å2
Refinement stepCycle: LAST / Resolution: 1.95→58.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 19 86 1552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681493
X-RAY DIFFRACTIONf_angle_d0.8572023
X-RAY DIFFRACTIONf_chiral_restr0.0501220
X-RAY DIFFRACTIONf_plane_restr0.0084266
X-RAY DIFFRACTIONf_dihedral_angle_d15.9318561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.070.33691450.2912646X-RAY DIFFRACTION93.13
2.07-2.230.28181220.25812803X-RAY DIFFRACTION98.95
2.23-2.460.27571360.21642853X-RAY DIFFRACTION99.43
2.46-2.810.23971510.22322830X-RAY DIFFRACTION99.77
2.81-3.540.24211570.19672837X-RAY DIFFRACTION100
3.54-58.410.19171420.16882883X-RAY DIFFRACTION99.67
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)
15.37825705706-3.29825448657-0.262101571477.09026225111-0.2599526218842.95962762069-0.402644340048-0.699121609920.6896778774580.8404955648460.2129844824470.0094054771489-0.139361035177-0.4231694670770.1054232676740.2766698246490.0620570303604-0.009315590308110.337688774433-0.118191157070.29415851553934.3144075892-5.6788616394424.8419116466
25.64352153424-5.0977413414-1.267550506329.276692754462.728464493164.29042486530.099790637914-0.3988971103721.16892424368-0.258737751327-0.0175052440832-0.616311299551-0.418661185981-0.360598157226-0.2900453689830.466854395820.151737331130.007382191809080.502945923664-0.07419498583320.78941930614321.488982619210.075554894422.2727317322
36.089393268-3.2535737513-1.946648516287.25150739812.476689073295.211110547490.1557618516370.3891767996730.306772028304-0.740695646339-0.1352249161710.147461711187-0.375409201919-0.0381799316133-0.1194124134410.3468609277440.0118312258381-0.056827852130.3881927702060.0297212430480.34460770581929.4456177026-8.9922471326611.2337493707
48.57602628546-2.652692316160.4091114893082.69692567243-1.36107735452.340204063830.160465169320.2713851720331.12311438511-0.377370699384-0.1252594852980.282765200851-0.157626170092-0.5558882305730.004429341589620.4625748818030.0923732615096-0.1097181285930.376096285015-0.003674896340290.71582235010531.58992416762.82140994815.3812652323
56.0458292938-3.01715417848-1.081673857345.745236577561.398240260063.329619907350.0688014456740.3202001741780.58024734447-0.3967247991490.067145978073-0.120661493982-0.106420925528-0.215843479436-0.1189442873360.312079639975-0.0294951858973-0.02665376250570.3011428318530.07225281284880.27076790548934.1793874666-11.21487141479.80381122325
68.50141289288-1.38977815628-0.462705284248.31546053561.127117895627.8531835011-0.235085367928-0.460794277635-0.1019554209290.394787576736-0.01439370865330.7026473870390.372472507543-0.6171056125860.276800850170.23358085537-0.08496681253550.033774310450.3152245652750.0292943481030.28655132742329.6261037388-16.674686125719.7311864312
78.17021887785-3.18428754915-5.784347939877.65053578091-2.185965657457.221767562290.285936090460.430598349274-1.33344639396-0.688242205016-0.5170926654870.9488525191971.16196846073-1.918904905980.3170856734710.514079772636-0.0907779048505-0.346059939330.965841528955-0.05007179937950.98058549917117.3866010137-9.1506828972311.1515032509
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: B

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 154 through 183 )154 - 1831 - 30
22chain 'B' and (resid 184 through 197 )184 - 19731 - 43
33chain 'B' and (resid 198 through 211 )198 - 21144 - 57
44chain 'B' and (resid 212 through 251 )212 - 25158 - 97
55chain 'B' and (resid 252 through 280 )252 - 28098 - 126
66chain 'B' and (resid 281 through 314 )281 - 314127 - 160
77chain 'B' and (resid 315 through 336 )315 - 336161 - 180

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