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- PDB-9k76: Crystal structure of human STING in complex with F2W -

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Basic information

Entry
Database: PDB / ID: 9k76
TitleCrystal structure of human STING in complex with F2W
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / sting
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 / pattern recognition receptor signaling pathway / reticulophagy / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / protein complex oligomerization / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / positive regulation of DNA-binding transcription factor activity / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / antiviral innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / Regulation of innate immune responses to cytosolic DNA / protein serine/threonine kinase binding / positive regulation of interferon-beta production / autophagosome / cytoplasmic vesicle membrane / secretory granule 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 / endoplasmic reticulum membrane / protein kinase binding / 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: 2.1650155587 Å
AuthorsFeng, Z.W. / Zeng, T. / Chen, M.R. / Xiao, Y.B. / Xu, X.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82273786 China
CitationJournal: To Be Published
Title: Crystal structure of human STING in complex with F2W
Authors: Feng, Z.W. / Zeng, T. / Chen, M.R. / Xiao, Y.B. / Xu, X.L.
History
DepositionOct 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: 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)22,2732
Polymers21,8801
Non-polymers3941
Water1,02757
1
B: Stimulator of interferon genes protein
hetero molecules

B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5474
Polymers43,7592
Non-polymers7882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)81.371, 87.638, 73.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-401-

1T2

21B-514-

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: 21879.545 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 BL21(DE3) (bacteria) / References: UniProt: Q86WV6
#2: Chemical ChemComp-1T2 / 5-chloranyl-3-[(4-methylsulfonylphenyl)carbonylamino]-1-benzofuran-2-carboxylic acid


Mass: 393.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12ClNO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.99 Å3/Da / Density % sol: 63.11 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M calcium acetate, 20% w/v polyethylene glycol 3350, 0.1 M sodium acetate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.165→19.88 Å / Num. obs: 14129 / % possible obs: 98.45 % / Redundancy: 12.7 % / Biso Wilson estimate: 26.1913084607 Å2 / CC1/2: 0.995 / Net I/σ(I): 13.29
Reflection shellResolution: 2.165→2.242 Å / Num. unique obs: 1215 / CC1/2: 0.889

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F5W

4f5w


Resolution: 2.1650155587→19.8768541867 Å / SU ML: 0.294226245512 / Cross valid method: FREE R-VALUE / σ(F): 1.36394949779 / Phase error: 24.7831442348
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229505170079 1413 10.00779092 %
Rwork0.195279739919 12706 -
obs0.198679150196 14119 98.6170287071 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.0076014149 Å2
Refinement stepCycle: LAST / Resolution: 2.1650155587→19.8768541867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 26 57 1437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007273643777021407
X-RAY DIFFRACTIONf_angle_d0.8783857463491912
X-RAY DIFFRACTIONf_chiral_restr0.0467609930603211
X-RAY DIFFRACTIONf_plane_restr0.00501011667275247
X-RAY DIFFRACTIONf_dihedral_angle_d11.7908669545834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1650155587-2.24230.347886239811240.2790324652171085X-RAY DIFFRACTION86.3571428571
2.2423-2.33190.3006647343341440.2271374072411267X-RAY DIFFRACTION99.6468926554
2.3319-2.43790.2578943555171380.2074743935551270X-RAY DIFFRACTION99.9290276792
2.4379-2.56620.2557184507441280.2134656430071282X-RAY DIFFRACTION100
2.5662-2.72660.2574126138191580.2048427935771271X-RAY DIFFRACTION100
2.7266-2.93650.2324753017391470.1983321175891274X-RAY DIFFRACTION100
2.9365-3.23090.1940065961881460.1874012622361270X-RAY DIFFRACTION100
3.2309-3.69580.238695283811410.185908467781304X-RAY DIFFRACTION100
3.6958-4.64640.1927059624411370.1677297100981313X-RAY DIFFRACTION100
4.6464-19.87685418670.2073377023011500.1950592857931370X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.8896588346 Å / Origin y: -23.853957165 Å / Origin z: 8.560583404 Å
111213212223313233
T0.210228527087 Å20.0183241424945 Å20.00785478024281 Å2-0.227198789276 Å20.00603787329236 Å2--0.234877357844 Å2
L1.3066401123 °21.09176616563 °21.12466010145 °2-1.5697673364 °21.10066713855 °2--1.95641166454 °2
S-0.0503076538829 Å °0.0560285317828 Å °0.120578124815 Å °-0.053870939516 Å °-0.012077793768 Å °0.109525410116 Å °-0.00846976156238 Å °-0.0763596131064 Å °0.0689828545218 Å °
Refinement TLS groupSelection details: all

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