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- PDB-9wh9: Crystal Structure of Bovine STING bound to diABZI3 -

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Basic information

Entry
Database: PDB / ID: 9wh9
TitleCrystal Structure of Bovine STING bound to diABZI3
ComponentsStimulator of interferon genes protein
KeywordsSIGNALING PROTEIN / STING / diABZI3
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 / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / cGAS/STING signaling pathway / proton channel activity / Neutrophil degranulation / reticulophagy ...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 / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / cGAS/STING signaling pathway / proton channel activity / Neutrophil degranulation / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / signaling adaptor activity / activation of innate immune response / positive regulation of interferon-beta production / autophagosome / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm / protein homodimerization activity / plasma membrane / cytoplasm
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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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
A: Stimulator of interferon genes protein
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3483
Polymers44,4982
Non-polymers8501
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-13 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.997, 57.544, 136.378
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 genes protein / STING / Transmembrane protein 173


Mass: 22249.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: STING1, STING, TMEM173 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2KI99
#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: isolated from a natural source / 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.: 124 / 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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES sodium pH7.5, 0.8M Sodium phosphate monobasic monohydrate, 0.8M Potassium phosphate monobasic

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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: 1.81→68.19 Å / Num. obs: 32651 / % possible obs: 98.7 % / Redundancy: 11.4 % / CC1/2: 0.999 / Net I/σ(I): 11.9
Reflection shellResolution: 1.81→1.91 Å / Num. unique obs: 4309 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→29.33 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 1573 4.88 %
Rwork0.1999 30678 -
obs0.2029 32251 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.11 Å2 / Biso mean: 50.0979 Å2 / Biso min: 19.99 Å2
Refinement stepCycle: final / Resolution: 1.81→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 54 124 3032
Biso mean--26.9 46.66 -
Num. residues----356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.870.37971090.36442283239280
1.87-1.940.36121330.31062637277095
1.94-2.020.36531300.269628052935100
2.02-2.110.27611450.220328192964100
2.11-2.220.25891570.209928182975100
2.22-2.360.26891410.20528192960100
2.36-2.540.26511290.219228492978100
2.54-2.790.30611510.232228523003100
2.79-3.20.27241470.219628793026100
3.2-4.030.22751580.173128863044100
4.03-29.330.23211730.165330313204100
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)
16.81095.20072.47319.74484.2875.33760.13240.0269-0.364-0.02550.0126-0.23430.35420.4195-0.15050.31760.0518-0.02140.2114-0.00240.18-7.3225-7.871518.0178
23.93115.51261.17067.74832.4492.36440.2996-0.1895-0.26020.4751-0.0771-0.5778-0.08820.3033-0.23440.3489-0.017-0.04180.2856-0.01480.2660.82545.436731.5118
36.75736.69615.42399.17936.93155.2957-0.0134-0.33850.987-0.1881-0.79751.2285-0.6235-1.5280.73550.56960.13520.00310.48440.01040.4099-18.71681.978931.9911
45.26572.36193.16766.61020.07182.49360.1330.46970.6282-0.84950.21560.0838-0.83390.3966-0.29320.538-0.02920.01580.21630.02020.2581-5.80149.799427.1351
57.07620.4074-5.07484.8181.03893.98710.3865-0.84770.21860.4657-0.13540.0921-0.37920.9909-0.21790.4056-0.04880.01110.2606-0.06120.2304-8.47386.91841.089
66.20333.61934.87564.77462.69568.4389-0.0643-0.00470.3027-0.1492-0.09030.4948-0.0974-0.55890.21030.270.0540.02690.25090.00330.2567-18.5304-2.905926.1308
72.4516-0.2174-1.864.33931.14196.01530.1655-0.3492-0.63080.1277-0.19970.37940.6819-0.31070.08020.5015-0.0194-0.06850.25430.01440.2768-15.1555-14.96224.8127
83.30351.33254.05323.6874-0.40526.5418-0.02960.1748-0.5358-0.5202-0.1307-0.92210.51051.04440.28980.51970.05230.12120.3491-0.00340.4257-2.5197-7.845328.6189
92.3002-2.3179-0.7514.5276-0.59061.0706-0.5948-0.68370.24680.8745-0.90743.38480.0161-3.75971.14580.7377-0.07080.17031.4845-0.26441.0595-22.8167-6.420441.3322
103.0426-2.66143.71397.172-1.0596.13320.0715-0.4749-0.38580.8119-0.0767-0.46350.29260.4276-0.1090.53790.0256-0.06570.37530.00990.2631-3.5312-5.155942.0058
115.99420.0052-1.3574.194-3.62853.5390.0382-0.0747-0.4588-0.3238-0.17620.26010.6618-0.18990.14860.4985-0.0232-0.04790.27890.01150.1928-19.3299-7.820711.2563
125.15330.2754-1.2089.84-5.59063.42980.18650.54420.74690.50450.2010.1902-0.8250.0007-0.18690.48990.06490.00230.32290.02690.2566-20.898612.9394.2118
132.85562.0867-2.36488.1985-0.27525.66440.31940.33380.3033-0.4227-0.137-0.5457-0.23810.2661-0.12010.4533-0.0027-0.06590.44220.07580.2862-12.20254.0279-4.4616
143.43830.6209-1.04387.2492-0.2493.6230.2260.33620.4831-0.1392-0.0658-0.2451-1.0263-0.5091-0.19490.31960.05590.03580.24540.04980.3102-10.8159.8321-4.2923
152.6641-4.92660.58129.2392-0.89052.022-0.3172-0.2719-0.1751.00720.6154-0.55010.72760.555-0.24680.45950.1263-0.0770.4507-0.08550.321-7.7028-10.16887.1565
161.831-1.1958-1.94993.78980.25872.47860.412-0.78120.48070.0586-0.2046-0.25351.22190.68320.15881.2720.3511-0.12791.129-0.14591.1021-3.4194-19.125411.0192
172.9437-2.6723-4.50516.44572.05238.1390.04530.3971-0.7437-0.1382-0.2270.16821.16560.04170.12970.5743-0.0417-0.0890.3492-0.07060.3025-17.8821-13.96553.2374
184.18432.6264-3.1564.8215-1.45979.43020.25321.09270.4508-0.16250.02190.9369-0.399-1.6209-0.15410.47780.0304-0.05380.51180.05280.3899-23.6553-0.4415-0.0674
193.4949-3.36551.45469.7071.96012.7069-0.21340.9463-0.2748-0.431-0.2433-1.72170.66870.03330.4470.77350.07060.09290.507-0.060.4769-5.6186-9.2192-13.2033
203.1237-2.13813.62876.9456-0.68894.9602-0.0620.5374-0.4004-1.0013-0.00791.1293-0.3017-1.6462-0.01540.59560.0289-0.11280.86230.00550.3755-20.9641.6769-13.2917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 154 through 174 )A154 - 174
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 203 )A175 - 203
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 218 )A204 - 218
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 242 )A219 - 242
5X-RAY DIFFRACTION5chain 'A' and (resid 243 through 251 )A243 - 251
6X-RAY DIFFRACTION6chain 'A' and (resid 252 through 280 )A252 - 280
7X-RAY DIFFRACTION7chain 'A' and (resid 281 through 301 )A281 - 301
8X-RAY DIFFRACTION8chain 'A' and (resid 302 through 314 )A302 - 314
9X-RAY DIFFRACTION9chain 'A' and (resid 315 through 324 )A315 - 324
10X-RAY DIFFRACTION10chain 'A' and (resid 325 through 341 )A325 - 341
11X-RAY DIFFRACTION11chain 'B' and (resid 154 through 167 )B154 - 167
12X-RAY DIFFRACTION12chain 'B' and (resid 168 through 185 )B168 - 185
13X-RAY DIFFRACTION13chain 'B' and (resid 186 through 218 )B186 - 218
14X-RAY DIFFRACTION14chain 'B' and (resid 219 through 261 )B219 - 261
15X-RAY DIFFRACTION15chain 'B' and (resid 262 through 272 )B262 - 272
16X-RAY DIFFRACTION16chain 'B' and (resid 273 through 280 )B273 - 280
17X-RAY DIFFRACTION17chain 'B' and (resid 281 through 301 )B281 - 301
18X-RAY DIFFRACTION18chain 'B' and (resid 302 through 314 )B302 - 314
19X-RAY DIFFRACTION19chain 'B' and (resid 315 through 324 )B315 - 324
20X-RAY DIFFRACTION20chain 'B' and (resid 325 through 342 )B325 - 342

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