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- PDB-7x9q: Crystal structure of human STING complexed with compound BSP16 -

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Basic information

Entry
Database: PDB / ID: 7x9q
TitleCrystal structure of human STING complexed with compound BSP16
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / STING agonists
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
Chem-A9X / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPan, L. / Guan, X. / Feng, X. / Li, Z. / Bian, J.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31860245 China
National Natural Science Foundation of China (NSFC)31960203 China
National Natural Science Foundation of China (NSFC)82073702 China
National Natural Science Foundation of China (NSFC)32070387 China
National Natural Science Foundation of China (NSFC)81872746 China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of Selenium-Containing STING Agonists as Orally Available Antitumor Agents.
Authors: Feng, X. / Pan, L. / Qian, Z. / Liu, D. / Guan, X. / Feng, L. / Song, B. / Xu, X. / Tan, N. / Ma, Y. / Li, Z. / Wang, Z. / Bian, J.
History
DepositionMar 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)26,3902
Polymers26,0201
Non-polymers3691
Water724
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7794
Polymers52,0412
Non-polymers7392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3490 Å2
ΔGint-21 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.649, 54.502, 101.943
Angle α, β, γ (deg.)90.000, 98.400, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Stimulator of interferon genes protein / hSTING / Endoplasmic reticulum interferon stimulator


Mass: 26020.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q86WV6
#2: Chemical ChemComp-A9X / (2R)-4-(5,6-dimethoxy-1-benzoselenophen-2-yl)-2-ethyl-4-oxidanylidene-butanoic acid


Mass: 369.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18O5Se / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.78 Å3/Da / Density % sol: 30.78 % / Mosaicity: 0.36 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.4→47.95 Å / Num. obs: 12879 / % possible obs: 98.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 53.1 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.059 / Rrim(I) all: 0.102 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.492.90.64421317370.650.4450.7861.999.8
8.98-47.952.50.0583571410.9840.0440.07419.694.4

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UKM

6ukm


Resolution: 2.4→33.08 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 702 5.45 %
Rwork0.2135 12177 -
obs0.2163 12879 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.9 Å2 / Biso mean: 69.4296 Å2 / Biso min: 28.28 Å2
Refinement stepCycle: final / Resolution: 2.4→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 22 4 1400
Biso mean--36.29 55.99 -
Num. residues----179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.580.33011270.31162508263595
2.59-2.850.36511640.27082449261394
2.85-3.260.29841700.25452452262293
3.26-4.10.28971250.21252354247988
4.1-33.080.20951160.1752414253090

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