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- PDB-6cy7: Human Stimulator of Interferon Genes -

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Basic information

Entry
Database: PDB / ID: 6cy7
TitleHuman Stimulator of Interferon Genes
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / human STING / complex / cyclic-di-AMP / TMEM173 / Ala230 allelle / 230A/232R
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 / positive regulation of interferon-beta production / protein serine/threonine kinase binding / 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 / protein kinase binding / endoplasmic reticulum membrane / 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
Stimulator of interferon genes protein / : / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / IMIDAZOLE / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFernandez, D. / Li, L. / Ergun, S.L.
Citation
Journal: Cell / Year: 2019
Title: STING Polymer Structure Reveals Mechanisms for Activation, Hyperactivation, and Inhibition.
Authors: Ergun, S.L. / Fernandez, D. / Weiss, T.M. / Li, L.
#1: Journal: Biorxiv / Year: 2019
Title: STING polymer structure reveals mechanisms for activation, hyperactivation, and inhibition
Authors: Ergun, S.L. / Fernandez, D. / Weiss, T.M. / Li, L.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Aug 7, 2019Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _citation.journal_id_ISSN ..._chem_comp.name / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)27,9574
Polymers27,1381
Non-polymers8203
Water91951
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9148
Polymers54,2752
Non-polymers1,6396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_643y+1,x-1,-z-21
Buried area4100 Å2
ΔGint-15 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.457, 111.457, 35.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-402-

IMD

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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: 27137.619 Da / Num. of mol.: 1 / Fragment: UNP residues 139-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM173, ERIS, MITA, STING / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WV6
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.32 % / Description: Rod
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium citrate tribasic, imidazole, PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2018
RadiationMonochromator: Liquid nitrogen-cooled double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→37 Å / Num. obs: 11912 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.029 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1696 / CC1/2: 0.759 / Rpim(I) all: 0.305 / Rrim(I) all: 0.726 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LOH

4loh


Resolution: 2.2→20.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.045 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.212 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25753 594 5 %RANDOM
Rwork0.20238 ---
obs0.2052 11264 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.2→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 31 51 1506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191496
X-RAY DIFFRACTIONr_bond_other_d0.0020.021345
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.9882027
X-RAY DIFFRACTIONr_angle_other_deg1.14833114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2335177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1162480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.35615250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6931514
X-RAY DIFFRACTIONr_chiral_restr0.1370.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211654
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02312
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9825.213709
X-RAY DIFFRACTIONr_mcbond_other4.985.212708
X-RAY DIFFRACTIONr_mcangle_it7.1967.772881
X-RAY DIFFRACTIONr_mcangle_other7.1937.774882
X-RAY DIFFRACTIONr_scbond_it5.4895.569787
X-RAY DIFFRACTIONr_scbond_other5.4885.569787
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8998.2011145
X-RAY DIFFRACTIONr_long_range_B_refined10.70660.2091623
X-RAY DIFFRACTIONr_long_range_B_other10.70960.2051622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.198→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 37 -
Rwork0.285 816 -
obs--100 %

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