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- PDB-9qvt: Crystal structure of STING CTD in complex with potent agonist D5 -

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Basic information

Entry
Database: PDB / ID: 9qvt
TitleCrystal structure of STING CTD in complex with potent agonist D5
ComponentsStimulator of interferon genes protein
KeywordsSIGNALING PROTEIN / STING / Immune System / cGAS / agonist / interferon / signalling
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: 2.305 Å
Authorsdos Reis, C.V. / Hsu, N.-S. / Rooney, T. / Skidmore, J. / Bernardes, G.J.L. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Alzheimers Research UK (ARUK)ARUK-2015DDI-CAM United Kingdom
CitationJournal: Nat.Chem. / Year: 2025
Title: Tumour-specific STING agonist synthesis via a two-component prodrug system.
Authors: Hsu, N.S. / Tang, C. / Mendes, R.V. / Labao-Almeida, C. / Dos Reis, C.V. / Coelho, A.R. / Marques, M.C. / Cabeza Cabrerizo, M. / Misteli, R. / Rooney, T.P.C. / Hyvonen, M. / Corzana, F. / ...Authors: Hsu, N.S. / Tang, C. / Mendes, R.V. / Labao-Almeida, C. / Dos Reis, C.V. / Coelho, A.R. / Marques, M.C. / Cabeza Cabrerizo, M. / Misteli, R. / Rooney, T.P.C. / Hyvonen, M. / Corzana, F. / Fior, R. / Bernardes, G.J.L.
History
DepositionApr 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7592
Polymers27,1551
Non-polymers6051
Water48627
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5194
Polymers54,3092
Non-polymers1,2092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3410 Å2
ΔGint-19 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.681, 75.595, 34.138
Angle α, β, γ (deg.)90.00, 97.75, 90.00
Int Tables number5
Space group name H-MC121

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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: 27154.564 Da / Num. of mol.: 1 / Mutation: L139S,H232R
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-A1JA0 / 4-[6-methoxy-5-[[6-methoxy-2-(4-oxidanyl-4-oxidanylidene-butanoyl)-1-benzothiophen-5-yl]sulfanylmethylsulfanyl]-1-benzothiophen-2-yl]-4-oxidanylidene-butanoic acid


Mass: 604.735 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H24O8S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.74 Å3/Da / Density % sol: 55.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NaNO3 (Salt) 20 %w/v PEG 3350 (Precipitant) 10 %v/v EG (Precipitant) 0.1 M BIS-TRIS prop 7.5 pH (Buffer)
Temp details: 293

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 13, 2025
RadiationMonochromator: double-crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.305→57.58 Å / Num. obs: 6416 / % possible obs: 82.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 51.69 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Net I/σ(I): 10.2
Reflection shellResolution: 2.305→2.575 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.474 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 321 / CC1/2: 0.586 / Rpim(I) all: 0.587 / Rrim(I) all: 1.587 / % possible all: 40.4

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (10-JUL-2024)refinement
PDB_EXTRACT1.4.3data extraction
autoPROC1.0.5data reduction
Aimless0.8.2data scaling
BUSTER2.10.4 (10-JUL-2024)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.305→57.579 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3881 300 -RANDOM
Rwork0.3422 ---
obs-6416 82.3 %-
Refinement stepCycle: LAST / Resolution: 2.305→57.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 39 27 1349
LS refinement shellResolution: 2.305→2.575 Å / Num. reflection obs: 2321

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