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- PDB-11gn: Crystal structure of mSTING in complex with 3'3'-di-AMP -

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Basic information

Entry
Database: PDB / ID: 11gn
TitleCrystal structure of mSTING in complex with 3'3'-di-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 / peroxisome / regulation of gene expression / regulation of inflammatory response / cilium / defense response to virus / ciliary basal body / RNA polymerase II-specific DNA-binding transcription factor binding / 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
Chem-2BA / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsKranzusch, P.J. / Li, Y.
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 3'3'-di-AMP
Authors: Kranzusch, P.J. / Li, Y.
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
D: Stimulator of interferon genes protein
E: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2997
Polymers84,9204
Non-polymers1,3793
Water14,970831
1
A: Stimulator of interferon genes protein
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1193
Polymers42,4602
Non-polymers6581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-18 kcal/mol
Surface area15040 Å2
MethodPISA
2
D: Stimulator of interferon genes protein
E: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1814
Polymers42,4602
Non-polymers7202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-16 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.970, 74.504, 96.439
Angle α, β, γ (deg.)90.000, 93.213, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 21230.072 Da / Num. of mol.: 4
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-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / 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 % sol: 35.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM lithium acetate, 20% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.11586 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11586 Å / Relative weight: 1
ReflectionResolution: 1.29→44.9 Å / Num. obs: 158419 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 0.997 / Net I/σ(I): 8
Reflection shellResolution: 1.29→1.31 Å / Num. unique obs: 14759 / CC1/2: 0.537

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→44.9 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2037 1992 1.26 %
Rwork0.1786 156043 -
obs0.1789 158035 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.72 Å2
Refinement stepCycle: LAST / Resolution: 1.29→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5773 0 92 831 6696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00936146
X-RAY DIFFRACTIONf_angle_d1.14918353
X-RAY DIFFRACTIONf_chiral_restr0.081910
X-RAY DIFFRACTIONf_plane_restr0.0111097
X-RAY DIFFRACTIONf_dihedral_angle_d12.67212326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.320.37031260.329810181X-RAY DIFFRACTION90.58
1.32-1.360.331480.289711084X-RAY DIFFRACTION98.97
1.36-1.40.3151390.268411059X-RAY DIFFRACTION98.97
1.4-1.440.22411440.240811162X-RAY DIFFRACTION99.24
1.44-1.490.2691360.217911143X-RAY DIFFRACTION99.41
1.49-1.550.23471410.207411194X-RAY DIFFRACTION99.51
1.55-1.620.19841420.200611192X-RAY DIFFRACTION99.89
1.62-1.710.20761440.180811224X-RAY DIFFRACTION100
1.71-1.820.20051400.173211257X-RAY DIFFRACTION99.99
1.82-1.960.18911540.168811247X-RAY DIFFRACTION99.97
1.96-2.150.17621460.151811245X-RAY DIFFRACTION99.97
2.15-2.470.18271470.150311278X-RAY DIFFRACTION99.96
2.47-3.110.1791400.159611317X-RAY DIFFRACTION99.94
3.11-44.90.18271450.155911460X-RAY DIFFRACTION99.98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.720544578790.5876114766960.5057831610712.609265896541.753255979172.82268858231-0.01403521383730.05202404849430.0145845788247-0.127320119550.0306737497796-0.03383457758160.01967242733210.0284471862272-0.006505981080070.0854591964512-0.007443141573880.006735399244650.07048287411210.004294145695980.053950893704772.6029940684-5.0812998282-9.59065411065
22.49874083554-0.372667005168-0.8865801152082.289590174211.053230027382.227679640250.01644548620150.163675461982-0.171597007506-0.35314641455-0.09639062293330.273676617046-0.181556268516-0.08461699298460.106338623310.1026096974270.016365944276-0.03957719096060.09259126566850.009363836458510.11912987184461.1492290882-9.5517315264-12.0429122974
36.41085920990.234624143387-0.3687615482531.82067123840.1373445424250.832027464256-0.0739488131710.174709688610.0504801465501-0.09909811763610.06270076746170.3087889312420.0228135929335-0.0848262176060.01671409568950.0910641663802-0.00633060381227-0.01774644146180.07896794691970.01087464474480.091183687395262.3990704143-16.8071312768-9.30835857975
41.25820885831-0.1062521693850.1283137062651.240880772910.2418796475721.122419220390.0240047279087-0.0786685949717-0.00769222574623-0.0337752861521-0.03496812978480.170651598166-0.0642225123665-0.1378218545460.0106246014280.0585935020025-0.001586915175120.004916065839410.07329862628070.0009701601498110.07286042969564.6711972019-8.71426899117-2.78403570091
55.08530080112-0.704927655667-2.918532438072.890413314210.4795848978236.215789157010.0423843118189-0.1032795155280.308433106196-0.226654932835-0.1134606988940.568203229602-0.408622411797-0.186848519574-0.1854174655330.1406579827940.0120352184749-0.03117890018090.0937245781008-0.0551907705760.20164499542162.58624716467.21938766667-2.27140401383
64.668451304451.91515479392-4.140962169243.09342361012-1.447045397195.90345852535-0.1775576085540.08789125312690.00862886164188-0.329757169490.05953458290930.1848171441880.04266772236420.08450413755740.1238584714610.1218874844550.00746107028218-0.03226039261340.07653748634190.02527731230110.074949367441865.93034790940.576490717918-14.2776297994
75.75368351683-4.55929583164-5.610643806954.751987715393.461115297916.414523766050.07021740916180.0233990339663-0.4201493458830.107562652108-0.1553779913670.009226847767910.09219820512280.1068331551880.07641450190460.1034929878480.0077534247931-0.01115118139110.1444386921180.02326332671690.22385038700844.3982896356-1.46363111524-4.71657842388
85.29254097503-1.06293387096-2.059553392243.774986044780.8333224351883.96367630651-0.1998510340050.7234476269640.45513780243-0.606307598197-0.2187907674270.396837242633-0.450489188201-0.1718223123450.166842069440.150005615536-0.0329369380619-0.1228224678160.2013396378710.04314980947890.23838871404953.1362785943-5.31965876582-16.8601601391
91.85460526258-0.7449621955150.0466629570143.10841807518-0.7070139895891.177311560630.00119972535542-0.121932101768-0.2284554914150.1986836522960.009051728824780.07525222083740.1269786197730.0696183015549-0.02303121753270.0902378632718-0.00129601592677-0.005499851505320.09932632348290.0207372689690.086101109834773.8850003005-12.810608847711.1186708957
101.9581961067-0.632980510287-0.1332379812391.709554743730.5004828679931.72650614328-0.0174522796414-0.236576677561-0.04934051883690.2014684465260.0871668856214-0.09008012011380.1582553182180.230140553371-0.1138004054350.1051264138350.00468203124102-0.03034429820020.1547351992020.009927543764460.11697578058385.1423504574-11.665569595812.8655919731
112.14333809381-0.303224942160.4813428123251.103419843160.6556841148891.523374542160.00666670402784-0.0701701562405-0.01601934723880.09324190040150.148102608952-0.2504379137750.142545088510.277024499674-0.0774590980330.06807702479950.017825397565-0.01568023609870.118274247825-0.01145859936040.13631038697983.4217551069-16.30248187965.27598751095
120.840856783911-0.7634392327050.01111860505153.65803374051-0.7634963794991.848706221190.0269253343188-0.06626510793430.05453957576620.1245078568690.0684505950669-0.0941613341574-0.06025660599990.111052145603-0.03722392807070.0528286202076-0.0205889324565-0.01170047655680.113194615422-0.01862356529060.097689437845983.2713311734-0.96305180514.89759713475
134.28622461443.69670002209-3.256981428995.90242005619-3.841510752365.419104057420.300193500382-0.2410420194230.08851079006080.519212504012-0.180075510944-0.189147693247-0.3264849035180.232137345394-0.1201557000890.149091384019-0.0261965282147-0.007252083864620.12536234577-0.02129798473090.12632265152977.05222460324.1712078581914.6702392258
143.09962602830.6017724839550.2304686705921.307939254680.4346745788930.222028139265-0.0631702102479-0.565264735036-0.04883657824630.4680524077660.153652787138-0.07093636568860.2573316162480.30793596893-0.07902599459120.1626023219880.0197077194869-0.05514747682360.285319684472-0.0366279448780.092992802041285.2218833044-8.8111097465919.1686458486
151.27531145782-0.878903764207-1.074379340594.205363612072.601514060973.192801304110.064522659950.05212834612520.113229607217-0.0889390646425-0.0299156058668-0.133091663613-0.1442228714440.00635825581675-0.04439829241880.0424676210886-0.00344675072851-0.01723518554930.05929158912610.01267162405890.065247301282870.4556667498-10.580078930943.2980149162
163.382986410521.271212226081.014336893297.69791973614.939829235795.80279584067-0.02316505595340.242539607006-0.0244811413534-0.1715326184960.124565186169-0.02978365797750.04394955773480.0502835457855-0.05078481281350.113227251715-0.01002061215290.005662266134950.106465954598-0.02576726447650.042548917006969.9427091386-28.537115877328.2033978134
170.5632305839980.0289572927027-0.04086070296950.8964967552980.08350947825280.419219982296-0.01187649248360.0771593355169-0.0358665749359-0.152890025039-0.009829785824090.0626400690602-0.011039572942-0.02639766304650.01233341976020.06953324668490.000819493055456-0.01711590951980.0758093097173-0.01193851824010.05591606460363.1047134649-24.395874422238.4934334207
180.9479851611-0.338464842495-0.3053209045851.1645171132-0.03720841789530.9070230575960.0460743548520.0106455094025-0.0908848775615-0.188387646049-0.03184752703490.0904471009484-0.185205041551-0.19390230283-0.01792566809910.02014680138720.0125253929483-0.025174173830.08528362602090.002094985200570.073664021684156.8987949133-19.129106012244.956523716
196.12335520007-0.107434378508-4.065520396732.59494642050.2169600462736.621299348610.08824037073420.1294632530140.040539358841-0.0277220955845-0.09602170218390.0712766516181-0.260522968927-0.196307570157-0.05234905012720.04892129847130.00732138553351-0.02419795231860.0560258091468-0.01248963697790.072178366612960.2828786409-4.5732688301444.8488618737
202.87617702396-0.975282990381-1.58964765511.250951179520.8478593474272.261197283170.1069136525990.02127128161780.0820576836682-0.181509588328-0.007264174382340.155696490584-0.09992856090150.0420698234095-0.07893537670530.1179988064780.00788109439023-0.03539050473480.07442792404060.008699228608680.11089782364955.537395556-11.918274650436.746714887
213.859198574830.426883635859-0.6519804155593.79673365603-1.074773274627.414266663190.09715637594480.623939767760.331651029518-0.1860153447580.07014841054650.127239315545-0.331606055433-0.0946696818297-0.1270418428280.1529992628260.0296949334963-0.06291530922420.1849267099560.02067792146240.12317623260752.7732015593-16.156073826329.336726695
221.66623249476-1.534327947280.4672639716014.92999844519-0.701854688140.8837733765110.0558395797866-0.0278562353354-0.0642287364760.0123185041771-0.040800325557-0.03467391026280.0640135692307-0.0495191464813-0.003825378969510.0425069289499-0.00191126443381-0.01630972910820.0692934274149-0.006174480350610.04030821900571.3571663341-24.131711021358.6556943683
231.38199082916-0.6422591159260.3377334715733.37577845678-0.3621260393341.335600788540.109492870813-0.118030696159-0.1998547838380.419846254138-0.173634253014-0.276415777113-0.01161364149690.138315865712-0.01618739808770.04271059980120.0121807675307-0.04972988776680.1033327601590.009489318840440.14658721977882.7417680588-28.446605561962.4771852927
241.393836292680.3014820963540.2607729741670.639327657732-0.09234027543760.9422865959440.03102880678980.0154811711919-0.03370349662550.0330813425588-0.0452230004161-0.1680221237110.03600016267140.207451200839-0.04315439922910.04039305301190.00846556198006-0.01256331851310.09933680009656.69701465519E-50.11620759702883.0612649966-25.610174238453.6097005397
251.5809717907-0.363518594381-0.1203851754153.71582310811-0.9960779069622.02537965394-0.06162772887750.08041782846840.0948869925926-0.09571129202190.0271794593983-0.106078179982-0.138744246523-0.09739878282090.06068244406160.0748814107683-0.0159231309504-0.0169717067520.08475297319260.005771424508120.11423604146777.4573674261-4.436900101247.5550275517
264.331173984614.38505457788-3.985248771366.90806815815-4.890148236896.7901136363-0.039106482153-0.123312934093-0.0424250868280.259498191046-0.203683199711-0.376986233613-0.1109355166150.07584817406050.1782561039450.08089829647480.0181312271543-0.03786087843750.0661370774164-0.01991424332750.10133076536375.4807479005-7.1633513314661.4312635049
272.02402877160.1019433527210.2655749415941.099324428710.1954171383090.739465230880.0441784391618-0.5406241371680.2120593133090.280278981867-0.113413194355-0.1312605342950.007440981098320.1397799414290.01494759413450.138298569774-0.0238423157489-0.04876454705940.165763332426-0.01487465666190.11293169509183.712864345-19.975768413366.1140211545
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 151 through 184 )AA151 - 1841 - 34
22chain 'A' and (resid 185 through 210 )AA185 - 21035 - 60
33chain 'A' and (resid 211 through 229 )AA211 - 22961 - 79
44chain 'A' and (resid 230 through 279 )AA230 - 27980 - 126
55chain 'A' and (resid 280 through 300 )AA280 - 300127 - 147
66chain 'A' and (resid 301 through 313 )AA301 - 313148 - 160
77chain 'A' and (resid 314 through 323 )AA314 - 323161 - 170
88chain 'A' and (resid 324 through 334 )AA324 - 334171 - 181
99chain 'B' and (resid 151 through 185 )BB151 - 1851 - 35
1010chain 'B' and (resid 187 through 210 )BB187 - 21036 - 59
1111chain 'B' and (resid 211 through 250 )BB211 - 25060 - 99
1212chain 'B' and (resid 251 through 279 )BB251 - 279100 - 128
1313chain 'B' and (resid 280 through 300 )BB280 - 300129 - 149
1414chain 'B' and (resid 301 through 334 )BB301 - 334150 - 176
1515chain 'D' and (resid 151 through 173 )DD151 - 1731 - 23
1616chain 'D' and (resid 174 through 184 )DD174 - 18424 - 34
1717chain 'D' and (resid 185 through 241 )DD185 - 24135 - 91
1818chain 'D' and (resid 242 through 279 )DD242 - 27992 - 128
1919chain 'D' and (resid 280 through 300 )DD280 - 300129 - 149
2020chain 'D' and (resid 301 through 323 )DD301 - 323150 - 172
2121chain 'D' and (resid 324 through 336 )DD324 - 336173 - 185
2222chain 'E' and (resid 151 through 184 )EF151 - 1841 - 34
2323chain 'E' and (resid 185 through 202 )EF185 - 20235 - 52
2424chain 'E' and (resid 203 through 261 )EF203 - 26153 - 111
2525chain 'E' and (resid 262 through 279 )EF262 - 279112 - 129
2626chain 'E' and (resid 280 through 300 )EF280 - 300130 - 150
2727chain 'E' and (resid 301 through 334 )EF301 - 334151 - 178

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