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- PDB-6s27: Crystal structure of human wild type STING in complex with 2'3'-c... -

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Basic information

Entry
Database: PDB / ID: 6s27
TitleCrystal structure of human wild type STING in complex with 2'3'-cyclic-GMP-2'F-2'dAMP
ComponentsStimulator of interferon protein
KeywordsPROTEIN BINDING / Activator / Membrane protein / Immune system / Receptor
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / 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 / cGAS/STING signaling pathway / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / 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 / cGAS/STING signaling pathway / positive regulation of type I interferon-mediated signaling pathway / reticulophagy / pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / autophagosome assembly / cellular response to organic cyclic compound / 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 / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of interferon-beta production / secretory granule membrane / cytoplasmic vesicle membrane / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / protein complex oligomerization / positive regulation of protein binding / regulation of inflammatory response / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / RNA polymerase II-specific DNA-binding transcription factor binding / endosome / Golgi membrane / nucleotide binding / 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 / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'3'-cyclic-GMP-2'F-2'dAMP / Stimulator of interferon genes protein / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.802 Å
AuthorsSmola, M. / Boura, E.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
CitationJournal: J.Med.Chem. / Year: 2019
Title: Enzymatic Preparation of 2'-5',3'-5'-Cyclic Dinucleotides, Their Binding Properties to Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations.
Authors: Novotna, B. / Vanekova, L. / Zavrel, M. / Budesinsky, M. / Dejmek, M. / Smola, M. / Gutten, O. / Tehrani, Z.A. / Pimkova Polidarova, M. / Brazdova, A. / Liboska, R. / Stepanek, I. / Vavrina, ...Authors: Novotna, B. / Vanekova, L. / Zavrel, M. / Budesinsky, M. / Dejmek, M. / Smola, M. / Gutten, O. / Tehrani, Z.A. / Pimkova Polidarova, M. / Brazdova, A. / Liboska, R. / Stepanek, I. / Vavrina, Z. / Jandusik, T. / Nencka, R. / Rulisek, L. / Boura, E. / Brynda, J. / Pav, O. / Birkus, G.
History
DepositionJun 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8652
Polymers23,1891
Non-polymers6761
Water75742
1
A: Stimulator of interferon protein
hetero molecules

A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7314
Polymers46,3782
Non-polymers1,3532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3960 Å2
ΔGint-19 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.441, 111.441, 35.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

21A-537-

HOH

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Components

#1: Protein Stimulator of interferon protein


Mass: 23189.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING, LOC340061, hCG_1782396 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R3XZB7, UniProt: Q86WV6*PLUS
#2: Chemical ChemComp-KT8 / 2'3'-cyclic-GMP-2'F-2'dAMP


Mass: 676.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23FN10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Calcium Chloride, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.802→35.24 Å / Num. obs: 5811 / % possible obs: 99.25 % / Redundancy: 9.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1567 / Rpim(I) all: 0.05334 / Rrim(I) all: 0.1658 / Net I/σ(I): 14.86
Reflection shellResolution: 2.802→2.902 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.231 / Num. unique obs: 564 / CC1/2: 0.719 / Rpim(I) all: 0.4021 / Rrim(I) all: 1.297 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.03 Å35.24 Å
Translation5.03 Å35.24 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KSY

4ksy


Resolution: 2.802→35.24 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.02
RfactorNum. reflection% reflection
Rfree0.2761 582 10.01 %
Rwork0.2037 --
obs0.2109 5810 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.05 Å2 / Biso mean: 54.6592 Å2 / Biso min: 18.02 Å2
Refinement stepCycle: final / Resolution: 2.802→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 66 42 1481
Biso mean--34.7 46.82 -
Num. residues----172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8009-3.08260.42951400.29471262140298
3.0826-3.52830.31331430.237112871430100
3.5283-4.44390.25381450.175413021447100
4.4439-35.24350.23781540.18571382153699

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