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- PDB-8gjx: Structure of the human STING receptor bound to 2'3'-cUA -

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Basic information

Entry
Database: PDB / ID: 8gjx
TitleStructure of the human STING receptor bound to 2'3'-cUA
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / STING / cyclic dinucleotide / innate immunity / cGAS
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / proton channel activity / 2',3'-cyclic GMP-AMP binding / STING mediated induction of host immune responses / cyclic-di-GMP binding / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / proton channel activity / 2',3'-cyclic GMP-AMP binding / STING mediated induction of host immune responses / cyclic-di-GMP binding / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / reticulophagy / pattern recognition receptor signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / cellular response to organic cyclic compound / autophagosome assembly / autophagosome / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / activation of innate immune response / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / cytoplasmic vesicle membrane / positive regulation of DNA-binding transcription factor activity / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein complex oligomerization / regulation of inflammatory response / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173
Similarity search - Domain/homology
2'3'-cUA / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMorehouse, B.R. / Li, Y. / Slavik, K.M. / Toyoda, H. / 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: Cell / Year: 2023
Title: cGLRs are a diverse family of pattern recognition receptors in innate immunity.
Authors: Li, Y. / Slavik, K.M. / Toyoda, H.C. / Morehouse, B.R. / de Oliveira Mann, C.C. / Elek, A. / Levy, S. / Wang, Z. / Mears, K.S. / Liu, J. / Kashin, D. / Guo, X. / Mass, T. / Sebe-Pedros, A. / ...Authors: Li, Y. / Slavik, K.M. / Toyoda, H.C. / Morehouse, B.R. / de Oliveira Mann, C.C. / Elek, A. / Levy, S. / Wang, Z. / Mears, K.S. / Liu, J. / Kashin, D. / Guo, X. / Mass, T. / Sebe-Pedros, A. / Schwede, F. / Kranzusch, P.J.
History
DepositionMar 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9503
Polymers43,3152
Non-polymers6351
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-19 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.879, 110.879, 35.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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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: 21657.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING1, ERIS, MITA, STING, TMEM173 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WV6
#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.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium Sulfate, 0.1 M Tris pH 8.5, 16% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→49.59 Å / Num. obs: 13744 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 48.85 Å2 / CC1/2: 0.985 / Net I/σ(I): 7
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 1664 / CC1/2: 0.391

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.59 Å / SU ML: 0.4083 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2542 1352 9.94 %
Rwork0.2125 12256 -
obs0.2168 13608 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.89 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 42 56 2872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00192916
X-RAY DIFFRACTIONf_angle_d0.50753964
X-RAY DIFFRACTIONf_chiral_restr0.0387436
X-RAY DIFFRACTIONf_plane_restr0.0037508
X-RAY DIFFRACTIONf_dihedral_angle_d13.95031074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.46751260.30131185X-RAY DIFFRACTION95.62
2.69-2.80.3191260.28391175X-RAY DIFFRACTION97.38
2.8-2.930.33641330.2841205X-RAY DIFFRACTION97.95
2.93-3.080.27081330.25341214X-RAY DIFFRACTION99.78
3.08-3.280.2871350.2631224X-RAY DIFFRACTION99.93
3.28-3.530.27211400.21591237X-RAY DIFFRACTION100
3.53-3.880.26971370.19331219X-RAY DIFFRACTION100
3.88-4.450.20021370.17641246X-RAY DIFFRACTION100
4.45-5.60.24051360.1741244X-RAY DIFFRACTION100
5.6-49.590.19941490.20541307X-RAY DIFFRACTION99.93
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)
10.495934516455-0.5275440286990.4002732567560.6588445900180.0006083183841190.7502783896310.393210391193-0.0956206432146-0.167737863475-0.418305828725-0.129086921285-0.09232481345730.102965718056-0.2756340290440.006252779269630.449619702186-0.08151700884610.1249645654920.50429265625-0.03174624217440.421286131915-23.505054545426.6294723333-6.38846770032
23.700671498721.65214333737-0.9813392727082.31483149107-0.1211274127570.624957336012-0.4287067078091.854684608811.16910901488-1.371536309480.037186162229-0.4214106494220.4751857713990.494189440066-0.7087297609270.6800550728110.002906536714750.2646215361870.6443227829010.1428805705130.719427646143-6.1873777985434.9941492817-13.1907294432
33.16706004036-1.88115738235-0.5249089777581.711278169360.4393340911310.9669151769290.111547361123-0.238712818770.581341856945-0.190495064864-0.109000472203-0.5397748608650.09428777472060.189046474204-0.0003931402854350.448643261974-0.006984944938850.1033707003720.465861446761-0.009638972131850.583605429183-5.4671437951831.6863697568-1.71046771071
41.36398764616-0.4916190800481.337170101730.314986333558-0.03352451645091.12416351176-0.3051807356340.154083759834-0.3511627585220.06284987965440.109829295691-0.01371450434710.396142553638-0.432071199178-0.00480095955230.574871703749-0.01634668369760.1248597690370.41352580667-0.04048621813320.46507004421-16.057038759225.42046105465.00944665783
5-0.2041444991860.008658072679580.02223579095451.09039567873-0.4055266547370.039711640222-0.05648426847880.553976003785-0.630854074404-0.2484282200920.0565620865106-0.05507413503680.554798456124-1.56389518315-0.002189909572830.616824229197-0.07378679460680.03258843512510.499584170708-0.03433812525290.475391584853-21.353376537917.6865566499-2.67805623618
62.230643999880.682737733052-0.8934979264051.576605027030.9360169991411.100604554610.000392242415560.17633600148-0.575180170643-0.819237626383-0.0808521486395-0.3346475156210.3480420269670.2638181100020.03629575664780.6467022211960.1009351642460.21859480960.5101800592920.02092074800950.694080579498-9.9852330690319.8452689799-6.37207689541
70.6594559260.294165447319-0.1253416103330.5166652929010.1433182734410.155768022135-0.323417985061.06676758997-1.80887778828-0.476458884282-0.09890441525390.840479856090.805483394656-0.14542734773-0.001553545301930.7355823719880.1804474715150.05423398240530.706002867179-0.07754339579741.17097909382-0.44958256317817.1436286337-4.50777755749
80.486051325282-0.5327613690540.4750544719370.496245614538-0.6340900882290.8100162264170.0842380425017-0.110880036844-0.07538160513540.2041779152230.3601290355480.2962374546920.371241028248-0.1622868822210.001111932722830.493171743816-0.04155147776040.01319669425820.413227694466-0.1184895834540.468519044741-28.85635047531.94769368312.69959505086
91.73587944071-1.846064283040.1911441848834.416212102860.5367593809971.78152706215-0.21468819013-0.355401119860.558726638157-0.04780692460930.0819340930371-0.606605813561-0.249933683413-0.150881597667-0.002537588004980.419383931222-0.0279761482274-0.00248164863330.442702135857-0.1287642163210.55640468152-23.027840435549.79921088250.519072249695
100.701142214798-0.726406291250.2303978390771.23872440873-0.9436566002990.6821904725560.1255505868560.06605053210040.130917085348-0.1610511931-0.213681387362-0.02863808044930.285717496443-0.293545757415-0.01807386607850.4913034075830.007212198493470.03079917164320.519360529769-0.0998040810360.45165286036-30.034410761239.4362313379-8.73108513097
111.059551852620.09400450935110.0484383482998-0.191784755638-0.00748062070010.1302586347580.0120711418864-0.34815386568-0.2520446066260.1406515691990.1460391040890.5720198236520.439332673267-0.532773394649-0.0001254108143820.499228713638-0.0744579724360.02370552392440.53716448098-0.03499221772850.457161290718-37.752596130734.0609499821-1.06555351721
121.141048709190.797639811391-0.8357909091962.17603143083-0.02293807307381.094715407050.0452479475155-0.8944538335560.1942279233240.02208554100250.4098997884270.669720092066-0.301268158475-0.5768804825640.362039064120.4874623064940.0983632092857-0.06504905259060.67052561322-0.1386871054110.607319117858-35.586596704145.39883932312.6509124102
130.249202337224-0.0008355747111230.04009565712580.3058591329650.2351673954660.1985879298730.0275951222813-1.0216996198-0.3622866317810.5986289981090.1094745313091.2243193176-0.332556867623-0.838869433293-0.0007216954553790.6763177903830.1419509293580.00438293714260.730572052486-0.0961375610861.06432827499-38.231786665754.91791033170.911885158089
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 167 )AA153 - 1671 - 15
22chain 'A' and (resid 168 through 183 )AA168 - 18316 - 31
33chain 'A' and (resid 184 through 251 )AA184 - 25132 - 92
44chain 'A' and (resid 252 through 281 )AA252 - 28193 - 122
55chain 'A' and (resid 282 through 300 )AA282 - 300123 - 141
66chain 'A' and (resid 301 through 324 )AA301 - 324142 - 161
77chain 'A' and (resid 325 through 336 )AA325 - 336162 - 173
88chain 'B' and (resid 153 through 167 )BB153 - 1671 - 15
99chain 'B' and (resid 168 through 251 )BB168 - 25116 - 92
1010chain 'B' and (resid 252 through 281 )BB252 - 28193 - 122
1111chain 'B' and (resid 282 through 300 )BB282 - 300123 - 141
1212chain 'B' and (resid 301 through 324 )BB301 - 324142 - 161
1313chain 'B' and (resid 325 through 336 )BB325 - 336162 - 173

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