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- PDB-11gl: Crystal structure of mSTING in complex with 2'3'-cUMP-AMP -

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Basic information

Entry
Database: PDB / ID: 11gl
TitleCrystal structure of mSTING in complex with 2'3'-cUMP-AMP
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / Innate immunity / cGAS-STING / complex
Function / homology
Function and homology information


STING mediated induction of host immune responses / STING complex / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / protein exit from endoplasmic reticulum / Regulation of innate immune responses to cytosolic DNA / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of cGAS/STING signaling pathway ...STING mediated induction of host immune responses / STING complex / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / protein exit from endoplasmic reticulum / Regulation of innate immune responses to cytosolic DNA / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of cGAS/STING signaling pathway / positive regulation of type I interferon-mediated signaling pathway / proton channel activity / reticulophagy / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / protein complex oligomerization / positive regulation of macroautophagy / autophagosome membrane / cellular response to interferon-beta / autophagosome assembly / positive regulation of defense response to virus by host / positive regulation of type I interferon production / Neutrophil degranulation / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / signaling adaptor activity / positive regulation of interferon-beta production / autophagosome / antiviral innate immune response / protein serine/threonine kinase binding / regulation of gene expression / peroxisome / regulation of inflammatory response / cilium / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / ciliary basal body / mitochondrial outer membrane / transcription coactivator activity / endosome / Golgi membrane / innate immune response / lysosomal membrane / ubiquitin protein ligase binding / protein kinase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / identical protein binding / plasma membrane / cytosol / 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
2'3'-cUA / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLi, Y. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: To Be Published
Title: Crystal structure of mSTING in complex with 2'3'-cUMP-AMP
Authors: Li, Y. / Kranzusch, P.J.
History
DepositionFeb 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 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)42,9813
Polymers42,3462
Non-polymers6351
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-21 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.619, 46.735, 154.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Stimulator of interferon genes protein / mSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / MMITA / ...mSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / MMITA / Transmembrane protein 173


Mass: 21173.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sting1, Eris, Mita, Mpys, Sting, Tmem173 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3TBT3
#2: Chemical ChemComp-ZNT / 2'3'-cUA / 1-[(2R,5R,7R,8R,10S,12aR,14R,15R,15aS,16R)-14-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxooctahydro-2H,10H,12H-5,8-methano-2lambda~5~,10lambda~5~-furo[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-7-yl]pyrimidine-2,4(1H,3H)-dione


Mass: 635.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.95 Å3/Da / Density % sol: 36.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.5, 30% (w/v) PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.98→77.49 Å / Num. obs: 23875 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 46.1 Å2 / CC1/2: 0.998 / Net I/σ(I): 5.9
Reflection shellResolution: 1.98→2.09 Å / Num. unique obs: 1349 / CC1/2: 0.444

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→77.49 Å / SU ML: 0.4028 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.0684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2562 1151 5.09 %
Rwork0.2451 21449 -
obs0.2457 22600 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.85 Å2
Refinement stepCycle: LAST / Resolution: 1.98→77.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 42 34 2950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293020
X-RAY DIFFRACTIONf_angle_d0.61444100
X-RAY DIFFRACTIONf_chiral_restr0.0419448
X-RAY DIFFRACTIONf_plane_restr0.0048528
X-RAY DIFFRACTIONf_dihedral_angle_d14.39921120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.070.58961250.55571782X-RAY DIFFRACTION65.76
2.07-2.180.46641380.43792695X-RAY DIFFRACTION96.66
2.18-2.320.38811230.34932748X-RAY DIFFRACTION98.59
2.32-2.50.33261400.32562774X-RAY DIFFRACTION98.78
2.5-2.750.33651420.30322798X-RAY DIFFRACTION99.39
2.75-3.150.3011390.2832813X-RAY DIFFRACTION99.46
3.15-3.960.26011620.22172845X-RAY DIFFRACTION99.8
3.96-77.490.18351820.18622994X-RAY DIFFRACTION99.91
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)
18.766870946780.178069344726-0.6850666790345.443917239380.6050826969715.3276941723-0.163871124314-0.05392274254771.16603063369-0.346166119731-0.174357127321-0.0147797809677-1.1804281370.00691216647170.3827681645420.4686137465830.00508444192325-0.05991788218680.663638818207-0.1067097054660.66632294091315.526748938312.3899533806-24.6707684932
24.034529003432.521955967191.051293628885.843371991461.845782885372.34643594480.0430836614080.278300159463-0.498041781493-0.01143884275710.137559364968-0.7031873702450.2319522315490.447892899024-0.01463430699690.3845317496580.0154246242945-0.01087766386610.6457296693310.03289725518990.48164084917618.0504327696-6.13369037738-35.4749999564
32.87686890104-1.123357084230.3795414387346.417452894232.173485669152.852772749710.4255509384440.185968254984-0.000893548629753-1.09315066856-0.545811463375-0.213450788556-0.4359092904740.1970359105090.1698611914070.391316389642-0.0003600127284270.02598593929990.471771895523-0.0004956249651140.5186519686157.88031639275-6.25170709417-37.7764195738
43.884164472710.6809703496641.502646015421.381937588391.348352652561.786217782790.081911663159-1.34160537188-0.1584998376520.734049092461-0.4129628962171.509185281420.490588797233-0.1462098547960.264538534610.61536308932-0.02335215741090.1104831764370.8724292176150.04012967924690.691407671609-1.53367111494-2.53632466672-23.3110163187
55.08941745887-0.4035648683841.031024546142.442371631190.9675953203232.458199489250.158844009078-1.12777673536-1.745884016780.36743319857-0.223589583533-0.3236966476650.3176754709930.0410583955359-0.1073195768890.467943892535-0.0223423594250.001828587361010.4779836484090.1568928380360.69323339459911.8948803087-11.5229349161-29.1609224838
65.508114320360.6304563645791.477012793422.138817493871.478029711982.294568937540.074673929440.106844730201-0.2184325694840.139648120495-0.08235291785750.1310967362170.2193693897080.20808624484-0.06639166817590.387898376972-0.00914646367847-0.0008432379279090.5217773824280.1318838003380.414420831213.2414042588-7.11897807482-27.4590453165
74.65624600473-0.2690112054430.9695684097542.35588375137-0.9089167491972.86990759222-0.114295847301-1.395754628-0.04449130812450.548343151352-0.1998934748640.08752046593-0.21232602318-0.4478784842060.478392082410.355081021780.02131879240370.0811442564110.675563649107-0.03600451787770.4588453474494.232814281063.48084346146-20.8350103991
84.97535198031-0.853119718562-3.188108346075.638083050441.125248397887.598044124790.7447932140260.0150134389031.511134058490.0635212865063-0.1284545959560.494945375221-0.971071156743-0.959408584248-0.5805133282960.5170404399630.01725676341440.003034740531210.547715135075-0.1062565677860.7287450287066.5715198899114.8646008914-26.682103557
95.0989078842-0.4938982411551.209563946811.72454562893-1.217922464024.93291401705-0.3815548149720.712298318250.824507462649-0.59945017102-0.189999171402-0.0699409544719-0.3459613864760.911013903803-0.4431359167470.4425454092680.00582758538168-0.05737131089210.223397277357-0.09240150669890.64592823031210.20537101864.99857928087-37.5303701068
105.98244598802-0.7973773279740.1565049147962.714660206220.4269800899042.857155930110.123814645888-0.377791373074-0.1791780234470.0835952410904-0.3944297427660.397310086662-0.699900584306-0.0114079600205-0.1858872023380.462613463491-0.00563940426481-0.0686240222610.568921311053-0.04741357340020.623258651028-6.168757598832.01422558288-33.6359488112
116.797555027941.88387604821-1.475582749666.81856479706-2.014270639983.627131869140.198892048704-1.800519839960.3636972973260.280672909572-0.1918225358251.28283025497-0.143391168191-1.196323480090.04208477848990.6294072827110.0665325168679-0.02205443888921.50944218906-0.1566054620130.4988770622714.88671986725.24864500729-11.4515254248
120.262341944929-0.6475371171631.052106751112.32892485512-2.332623526814.054761223980.377990798196-0.463380145623-1.139219370810.636516319742-0.003174928033140.7523986291150.704762721323-0.1091089766250.4336090163420.787162109516-0.06755805448350.05012322790822.596650132720.8045659579870.49386045868623.0855786742-13.1232424458-5.12942983157
135.14946707973-3.35716487291.399625519689.09771315945-0.4099090823912.691368893310.261433292796-0.882929756146-1.384323632811.28839871348-0.842316805653-0.3130869080260.5822235244641.495598768910.3597270551310.9447669014490.0540120028304-0.1022296032062.25025599330.4807987241681.0023383683729.8083971298-12.5398943848-2.35966004629
141.54939433924-2.1463864122-1.405131418923.444950934321.717805444672.691685949270.600765705178-2.359752071121.26510056297-0.278193224921-0.224529029742-1.20853877199-0.3907969640360.2953381055690.3379100910020.502268157263-0.131343645562-0.06746718808171.89789376251-0.3658027628980.14209664409230.12122949386.23032179957-13.6770887678
153.42773612821.050118348170.1098528718681.940829176660.003690235279211.560401491420.358258529908-1.58553435297-1.218391252670.00509535728149-0.334244108615-0.4776947295050.3860218283120.755029825522-0.1583168905240.5442923174010.07037906631960.0243620911381.394409856250.2925853518720.57943829837628.1219636699-6.72667166818-14.8913673843
164.894020389640.542255126347-0.154406750334.40374933099-0.3386922644293.10966571454-0.157961820556-1.61967543411.172659193840.1536379412170.32691343756-0.230985160413-0.56004615553-0.165236772301-0.01408780166160.532931507855-0.0935993212045-0.02258293123551.33865901455-0.3805479683840.68573571102925.053678215211.7469146502-14.296208762
175.4444887545-0.3444266782411.377340029151.926378189691.62524444520.619619050188-0.115191869888-0.820339507516-0.4911985729572.245439840770.3057929416241.190087439430.0913511923408-0.124445439153-0.3524568181350.9447594402090.0804423159177-0.06370323672222.22580280739-0.05526179114490.52916616989324.05226797773.78147564423-2.653689131
187.38824790908-3.65175690862-4.480843553137.921461734351.033568275364.457999845140.0104284463571-1.463795420131.022545175160.593693604987-0.566658785497-0.716843578767-0.8491999103040.0979234748911-0.02396143775520.639443725267-0.0116750218106-0.01965407275152.15081562532-0.109068234870.6707826673838.28979991646.60268560634-4.7248266828
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 153 through 164 )AA153 - 1641 - 12
22chain 'A' and (resid 165 through 184 )AA165 - 18413 - 32
33chain 'A' and (resid 185 through 202 )AA185 - 20233 - 50
44chain 'A' and (resid 203 through 217 )AA203 - 21751 - 65
55chain 'A' and (resid 218 through 229 )AA218 - 22966 - 77
66chain 'A' and (resid 230 through 250 )AA230 - 25078 - 98
77chain 'A' and (resid 251 through 279 )AA251 - 27999 - 127
88chain 'A' and (resid 280 through 300 )AA280 - 300128 - 148
99chain 'A' and (resid 301 through 313 )AA301 - 313149 - 161
1010chain 'A' and (resid 314 through 334 )AA314 - 334162 - 182
1111chain 'B' and (resid 153 through 173 )BC153 - 1731 - 21
1212chain 'B' and (resid 174 through 182 )BC174 - 18222 - 30
1313chain 'B' and (resid 183 through 196 )BC183 - 19631 - 42
1414chain 'B' and (resid 197 through 210 )BC197 - 21043 - 56
1515chain 'B' and (resid 211 through 250 )BC211 - 25057 - 96
1616chain 'B' and (resid 251 through 300 )BC251 - 30097 - 146
1717chain 'B' and (resid 301 through 313 )BC301 - 313147 - 157
1818chain 'B' and (resid 314 through 334 )BC314 - 334158 - 175

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