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- PDB-8t5l: Crystal structure of STING CTD in complex with 2'3'-cGAMP -

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Basic information

Entry
Database: PDB / ID: 8t5l
TitleCrystal structure of STING CTD in complex with 2'3'-cGAMP
ComponentsStimulator of interferon genes protein
KeywordsANTIVIRAL PROTEIN / Mediator of IRF3 activation / Stimulator of interferon genes protein
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
cGAMP / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLi, Y. / Li, P. / Sun, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145287 United States
CitationJournal: Biorxiv / Year: 2023
Title: Structural and Biological Evaluations of a Non-Nucleoside STING Agonist Specific for Human STING A230 Variants.
Authors: Tang, Z. / Zhao, J. / Li, Y. / Tomer, S. / Selvaraju, M. / Tien, N. / Sun, D. / Johnson, D.K. / Zhen, A. / Li, P. / Wang, J.
History
DepositionJun 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2322
Polymers21,5571
Non-polymers6741
Water2,972165
1
B: Stimulator of interferon genes protein
hetero molecules

B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4634
Polymers43,1142
Non-polymers1,3492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4210 Å2
ΔGint-15 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.330, 79.230, 36.590
Angle α, β, γ (deg.)90.000, 96.130, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-652-

HOH

21B-666-

HOH

31B-751-

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: 21557.230 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 154-341)
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-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→39.61 Å / Num. obs: 16799 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.49 Å2 / CC1/2: 0.916 / Net I/σ(I): 8.2
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 1224 / CC1/2: 0.624

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4EMT

4emt


Resolution: 2.01→39.61 Å / SU ML: 0.2454 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.5575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2199 802 4.78 %
Rwork0.178 15987 -
obs0.1801 16789 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.95 Å2
Refinement stepCycle: LAST / Resolution: 2.01→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 45 165 1642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641508
X-RAY DIFFRACTIONf_angle_d0.90552051
X-RAY DIFFRACTIONf_chiral_restr0.0493225
X-RAY DIFFRACTIONf_plane_restr0.0071261
X-RAY DIFFRACTIONf_dihedral_angle_d17.2422553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.130.31241440.24532625X-RAY DIFFRACTION99.57
2.13-2.30.24231080.20042691X-RAY DIFFRACTION99.93
2.3-2.530.2551240.19822641X-RAY DIFFRACTION100
2.53-2.890.25181390.19972671X-RAY DIFFRACTION100
2.89-3.650.21611510.17012653X-RAY DIFFRACTION100
3.65-39.610.17971360.15362706X-RAY DIFFRACTION99.82
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)
13.38337302876-2.000427207570.8312570374385.808413272360.697666309731.28338853914-0.0322505619867-0.2577670701790.09367179559970.2124776466640.0169687899573-0.09340628195190.0620690567266-0.0365696988911-0.1364275845350.2276717448770.003851170291580.01732354631360.246471364257-0.008187381343650.1522584138737.9637921412-15.079561688722.7609863121
23.98595885228-3.59952224320.2709326335077.007180055440.6893810225262.43519273921-0.576616292516-0.6760206278950.6867624422260.8927532983390.4389405862640.089742635702-0.345369314803-0.3091331703820.1002132994170.3806641814550.08471140943590.03323647745430.398629978681-0.1228573154910.44285848584429.77400650333.755447553927.7326502723
39.8654131874-6.426911765550.681041399068.29855356078-0.2854477284814.21422967122-0.281273846632-0.2027846376910.8017919441090.17687223324-0.193460586455-0.205113911216-0.0865530417693-0.2038570845510.5252629494660.2971336603410.08783152146770.001464563434950.405715094067-0.05701163146130.56094617836320.74170089919.6134999389921.7200664972
43.3577790433-0.75714980852-0.4116755663332.585773766890.118830091261.148664195480.02778599181840.2378985586920.636034486964-0.237081159408-0.175049229780.453707786365-0.205941828139-0.3009487318590.1624113364040.2364992485910.0502869798955-0.02482182559390.2485383686490.01930147281550.34838792676429.0910948123-0.32292059463314.7875849476
57.9931534237-6.51134560673-4.479117739499.211133448965.328627465456.069450996220.1107532347330.5336044239780.495595032534-0.4431650311520.045372727973-0.4568652066270.1302667447080.00156269109228-0.1297906515850.219021979768-0.02880418091860.01510339900640.2274686469840.008616530167980.13410306617840.1511016493-17.64807248387.24642805613
67.15293993115-1.04276856575-0.652192688558.394389164165.049762268026.85794253046-0.00427021742410.279196410263-0.382540940326-0.01980972030070.0001480991831290.5994104248460.327889971168-0.4655356315960.03015426036480.197384947949-0.0396943439865-0.007579910745270.1958867602740.05592626301330.24210247035531.2015914295-20.902109669917.6622076938
72.371686737-0.9370627892731.608479589152.4980696416-0.2557203606647.456242353580.335226223235-0.841101158015-0.2383434493990.345966507533-0.2346267275620.5504156285990.879494004304-1.317808062190.1738576456280.381703236482-0.00847847870073-0.007163313512590.4783802916450.01474317734340.43463680439523.4899914563-10.716393154819.5196026418
83.96290058681-4.33190712986-0.6016826914155.077871193131.974877744298.58823022534-0.133253365929-0.321419420605-0.8107576008870.365484533697-0.06880600220441.755222497190.635947889013-0.8051443131990.08741501809470.298203346457-0.01415964034310.01141181297950.5258227510060.0258208289840.79519408772415.4735838605-6.26129206216.6444951878
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: B

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 154 through 167 )154 - 1671 - 14
22chain 'B' and (resid 168 through 185 )168 - 18515 - 32
33chain 'B' and (resid 186 through 197 )186 - 19733 - 44
44chain 'B' and (resid 198 through 262 )198 - 26245 - 109
55chain 'B' and (resid 263 through 280 )263 - 280110 - 127
66chain 'B' and (resid 281 through 301 )281 - 301128 - 148
77chain 'B' and (resid 302 through 324 )302 - 324149 - 165
88chain 'B' and (resid 325 through 336 )325 - 336166 - 177

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