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- PDB-9wh8: Crystal Structure of Human STING bound to diABZI3 -

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Basic information

Entry
Database: PDB / ID: 9wh8
TitleCrystal Structure of Human STING bound to diABZI3
ComponentsStimulator of interferon genes protein
KeywordsSIGNALING PROTEIN / STING / diABZI3
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / cGAS/STING signaling pathway ...STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / cGAS/STING signaling pathway / proton channel activity / reticulophagy / pattern recognition receptor signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / protein complex oligomerization / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / : / cellular response to interferon-beta / positive regulation of type I interferon production / positive regulation of defense response to virus by host / endoplasmic reticulum-Golgi intermediate compartment membrane / signaling adaptor activity / antiviral innate immune response / activation of innate immune response / positive regulation of interferon-beta production / protein serine/threonine kinase binding / autophagosome / secretory granule membrane / Regulation of innate immune responses to cytosolic DNA / cytoplasmic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / peroxisome / regulation of inflammatory response / defense response to virus / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / cilium / ciliary basal body / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / protein kinase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain
Similarity search - Domain/homology
: / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhao, Z.Z. / Li, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32373020 China
CitationJournal: To Be Published
Title: Species-Specific Regulation of STING by a C195 Disulfide Tetramer in Duck
Authors: Zhao, Z.Z. / Li, X.
History
DepositionAug 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3932
Polymers21,5431
Non-polymers8501
Water1,69394
1
B: Stimulator of interferon genes protein
hetero molecules

B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7864
Polymers43,0862
Non-polymers1,7002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)62.763, 62.763, 219.376
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-544-

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: 21543.205 Da / Num. of mol.: 1
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-A1AZ0 / 1-[(2E)-4-{5-carbamoyl-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-7-methoxy-1H-1,3-benzimidazol-1-yl}but-2-en-1-yl]-2-[(1-ethyl-3-methyl-1H-pyrazole-5-carbonyl)amino]-7-[3-(morpholin-4-yl)propoxy]-1H-1,3-benzimidazole-5-carboxamide


Mass: 849.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H51N13O7
Details: Author stated: In the complex, the morpholine ring of diABZI3 is highly flexible and thus poorly ordered in the electron-density maps, precluding reliable modeling.
Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 57.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M Imidazole pH6.5, 1M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→219.38 Å / Num. obs: 21256 / % possible obs: 100 % / Redundancy: 36.6 % / CC1/2: 1 / Net I/σ(I): 21.5
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 1504 / CC1/2: 0.875

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata scaling
DIALSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.14 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 1015 4.8 %
Rwork0.2097 20123 -
obs0.2121 21138 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.98 Å2 / Biso mean: 54.7593 Å2 / Biso min: 22.34 Å2
Refinement stepCycle: final / Resolution: 1.9→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 54 94 1535
Biso mean--29.15 54 -
Num. residues----172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-20.44421400.365427652905
2-2.130.29751570.257627902947
2.13-2.290.27921440.234727982942
2.29-2.520.27551420.226728552997
2.52-2.880.28781400.234728592999
2.88-3.630.27011420.214729153057
3.63-34.140.22951500.179131413291
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)
14.46016.2585-1.20669.1752-0.67283.05650.2314-0.5840.3940.6399-0.14760.88250.1111-0.2652-0.08720.27420.02140.05210.27750.09390.28833.7706-10.42596.5873
25.65774.53680.56114.33262.53936.30490.3555-0.83630.3553-0.0378-0.69160.80481.1235-1.9022-0.38820.6875-0.23160.06390.67730.21330.7738-7.405-26.86763.4133
32.91294.1407-0.44926.63510.5856.7177-0.42441.0696-0.1761-0.72410.28580.3372-0.2759-0.3947-0.0810.3484-0.0243-0.0060.40730.01070.32449.5596-14.6144-8.1781
44.9119-0.0429-1.16276.69923.20576.648-0.14640.38420.1819-0.25350.0630.75780.3231-0.41290.11910.3616-0.1128-0.09110.43150.1450.5115-2.009-19.4556-5.7916
57.6132.391-4.24664.5042-6.24878.8111-0.16620.45860.0418-0.81940.26020.04510.4013-0.183-0.10010.4105-0.01710.01030.292-0.01640.249817.0413-1.4528-11.2386
67.47591.9808-1.44787.4836-0.09968.0955-0.0346-0.3302-0.45780.30230.156-0.30480.5488-0.0049-0.10240.32050.0788-0.05750.22850.03340.278316.635-13.29751.3349
73.44143.326-1.57593.4289-0.73174.9322-0.76120.157-1.314-0.68520.5769-1.21871.4021.22990.14950.64650.09830.11390.5292-0.05980.730811.2238-27.1673-7.3851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 154 through 185 )B154 - 185
2X-RAY DIFFRACTION2chain 'B' and (resid 186 through 197 )B186 - 197
3X-RAY DIFFRACTION3chain 'B' and (resid 198 through 211 )B198 - 211
4X-RAY DIFFRACTION4chain 'B' and (resid 212 through 262 )B212 - 262
5X-RAY DIFFRACTION5chain 'B' and (resid 263 through 280 )B263 - 280
6X-RAY DIFFRACTION6chain 'B' and (resid 281 through 314 )B281 - 314
7X-RAY DIFFRACTION7chain 'B' and (resid 315 through 336 )B315 - 336

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