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- PDB-9whf: Crystal Structure of Duck STING bound to diABZI3 -

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Basic information

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


2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / defense response to virus ...2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / defense response to virus / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of 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 speciesAnas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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

Downloads & links

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Assembly

Deposited unit
A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8882
Polymers22,0381
Non-polymers8501
Water3,387188
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7764
Polymers44,0762
Non-polymers1,7002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)67.050, 67.050, 98.070
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-577-

HOH

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Components

#1: Protein Stimulator of interferon genes protein


Mass: 22038.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B9TBW9
#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.: 188 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Cesium chloride, 0.1 M MES monohydrate pH6.5, 30%v/v Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.65→67.05 Å / Num. obs: 27682 / % possible obs: 100 % / Redundancy: 25.6 % / CC1/2: 0.999 / Net I/σ(I): 17.1
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 1353 / CC1/2: 0.556

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.99 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 1484 5.38 %
Rwork0.1938 --
obs0.195 27609 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 0 188 1732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041582
X-RAY DIFFRACTIONf_angle_d0.7572149
X-RAY DIFFRACTIONf_dihedral_angle_d14.753590
X-RAY DIFFRACTIONf_chiral_restr0.045224
X-RAY DIFFRACTIONf_plane_restr0.004272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.31021200.32652341X-RAY DIFFRACTION100
1.7-1.760.33461290.28722347X-RAY DIFFRACTION100
1.76-1.830.28081320.25382309X-RAY DIFFRACTION100
1.83-1.920.23041510.22192335X-RAY DIFFRACTION100
1.92-2.020.25861300.20542334X-RAY DIFFRACTION100
2.02-2.150.26651470.20432337X-RAY DIFFRACTION100
2.15-2.310.21061190.18942379X-RAY DIFFRACTION100
2.31-2.540.19311450.18812344X-RAY DIFFRACTION100
2.54-2.910.22441330.19012402X-RAY DIFFRACTION100
2.91-3.670.20331340.17932430X-RAY DIFFRACTION100
3.67-29.990.18681440.17732567X-RAY DIFFRACTION100
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)
13.03371.2081-0.47373.8277-0.46012.8681-0.18280.1774-0.7215-0.36860.1055-0.54030.59710.2221-0.00070.25410.04440.010.195-0.04940.2976-5.4213-13.0982-31.0788
26.47560.82110.56866.81290.69795.90780.0807-0.0882-0.6837-0.0723-0.0374-0.72880.50450.11230.03110.21850.0549-0.04590.1743-0.00570.2885-4.0628-19.8054-28.4341
30.84280.75670.47582.94181.74782.06070.01350.0279-0.012-0.0005-0.08640.17470.0774-0.19440.0840.1278-0.001-0.02060.1810.00380.1833-15.1902-6.9358-27.6356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 157 through 221 )
2X-RAY DIFFRACTION2chain 'A' and (resid 222 through 265 )
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 344 )

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