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- PDB-8p45: Crystal structure of human STING in complex with the agonist MD1202D -

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Basic information

Entry
Database: PDB / ID: 8p45
TitleCrystal structure of human STING in complex with the agonist MD1202D
ComponentsStimulator of interferon genes protein
KeywordsANTIVIRAL PROTEIN / sting / antiviral / activator
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / 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 / protein complex oligomerization / positive regulation of macroautophagy / autophagosome membrane / cellular response to organic cyclic compound / autophagosome assembly / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / antiviral innate immune response / activation of innate immune response / positive regulation of interferon-beta production / endoplasmic reticulum-Golgi intermediate compartment membrane / autophagosome / Regulation of innate immune responses to cytosolic DNA / secretory granule membrane / positive regulation of DNA-binding transcription factor activity / cytoplasmic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / peroxisome / positive regulation of protein binding / 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-WY8 / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsKlima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Fluorinated cGAMP analogs, which act as STING agonists and are not cleavable by poxins: Structural basis of their function.
Authors: Klima, M. / Dejmek, M. / Duchoslav, V. / Eisenreichova, A. / Sala, M. / Chalupsky, K. / Chalupska, D. / Novotna, B. / Birkus, G. / Nencka, R. / Boura, E.
History
DepositionMay 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: 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.year
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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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)23,8832
Polymers23,1891
Non-polymers6941
Water00
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7654
Polymers46,3782
Non-polymers1,3872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3930 Å2
ΔGint-19 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.490, 77.980, 35.420
Angle α, β, γ (deg.)90.000, 97.580, 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

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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: 23189.064 Da / Num. of mol.: 1
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-WY8 / 9-[(1~{S},3~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one


Mass: 693.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23F2N9O8P2S2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium chloride; 100 mM HEPES pH 7.5; 20 % w/v PEG 4000; 10 mM spermine, 10 mM spermidine, 10mM ornithine, 10 mM 1,4-diaminobutane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.23→44.35 Å / Num. obs: 3917 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 90.47 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.3004 / Rpim(I) all: 0.08825 / Rrim(I) all: 0.3135 / Net I/σ(I): 8.2
Reflection shellResolution: 3.23→3.346 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.94 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 370 / CC1/2: 0.496 / CC star: 0.814 / Rpim(I) all: 0.7869 / Rrim(I) all: 2.096 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSxdsapp v3.1.9data reduction
XDSxdsapp v3.1.9data scaling
PHASER2.8.3phasing
Coot0.9.8.7model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.23→44.35 Å / SU ML: 0.3481 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.3148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 195 4.98 %random selection
Rwork0.2069 3722 --
obs0.2094 3917 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.15 Å2
Refinement stepCycle: LAST / Resolution: 3.23→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 44 0 1473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031505
X-RAY DIFFRACTIONf_angle_d0.55322049
X-RAY DIFFRACTIONf_chiral_restr0.0383224
X-RAY DIFFRACTIONf_plane_restr0.0039273
X-RAY DIFFRACTIONf_dihedral_angle_d11.9914595
LS refinement shellResolution: 3.23→44.35 Å
RfactorNum. reflection% reflection
Rfree0.2592 195 -
Rwork0.2069 3722 -
obs--99.95 %

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