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- PDB-7q3b: Crystal structure of human STING in complex with 3'3'-c-(2'F,2'dA... -

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Basic information

Entry
Database: PDB / ID: 7q3b
TitleCrystal structure of human STING in complex with 3'3'-c-(2'F,2'dA-isonucA)MP
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / sting / antiviral / activator
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
3'3'-c-(2'F,2'dA-isonucA)MP / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55733924728 Å
AuthorsSmola, M. / Klima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: Discovery of isonucleotidic CDNs as potent STING agonists with immunomodulatory potential.
Authors: Dejmek, M. / Sala, M. / Brazdova, A. / Vanekova, L. / Smola, M. / Klima, M. / Brehova, P. / Budesinsky, M. / Dracinsky, M. / Prochazkova, E. / Zavrel, M. / Simak, O. / Pav, O. / Boura, E. / ...Authors: Dejmek, M. / Sala, M. / Brazdova, A. / Vanekova, L. / Smola, M. / Klima, M. / Brehova, P. / Budesinsky, M. / Dracinsky, M. / Prochazkova, E. / Zavrel, M. / Simak, O. / Pav, O. / Boura, E. / Birkus, G. / Nencka, R.
History
DepositionOct 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: 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 1.2Aug 17, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3May 31, 2023Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4Feb 7, 2024Group: 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)23,8332
Polymers23,1891
Non-polymers6441
Water77543
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6674
Polymers46,3782
Non-polymers1,2892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4100 Å2
ΔGint-14 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.728, 110.728, 35.746
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

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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-8SC / 3'3'-c-(2'F,2'dA-isonucA)MP / 9-[(1R,6R,9R,10S,15R,17R,18R)-17-(6-aminopurin-9-yl)-18-fluoranyl-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-9-yl]purin-6-amine


Mass: 644.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23FN10O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Lithium acetate, 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: Aug 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.557→34.02 Å / Num. obs: 7594 / % possible obs: 100 % / Redundancy: 8.5 % / Biso Wilson estimate: 37.9884992619 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.2218 / Rrim(I) all: 0.2367 / Net I/σ(I): 7.7
Reflection shellResolution: 2.557→2.649 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.9621 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 716 / CC1/2: 0.777 / CC star: 0.935 / Rrim(I) all: 1.023 / % possible all: 98

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Processing

Software
NameVersionClassification
XDSxdsgui2data reduction
XDSxdsgui2data scaling
PHASER2.5.5phasing
Coot0.7.1model building
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ksy

4ksy


Resolution: 2.55733924728→34.0173257887 Å / SU ML: 0.282396223056 / Cross valid method: FREE R-VALUE / σ(F): 1.34751557498 / Phase error: 22.7504803796
RfactorNum. reflection% reflectionSelection details
Rfree0.231847861777 382 5.0309495588 %random selection
Rwork0.190811450839 7211 --
obs0.192989387043 7593 99.684915321 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.502334703 Å2
Refinement stepCycle: LAST / Resolution: 2.55733924728→34.0173257887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 43 43 1494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007082191915271487
X-RAY DIFFRACTIONf_angle_d1.076560267072026
X-RAY DIFFRACTIONf_chiral_restr0.0380045626748222
X-RAY DIFFRACTIONf_plane_restr0.0061980990071260
X-RAY DIFFRACTIONf_dihedral_angle_d13.548009796558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55733924728-2.92720.3037496415031240.221003095042335X-RAY DIFFRACTION99.5546558704
2.9272-3.68730.2209279610861250.1954796284362372X-RAY DIFFRACTION99.9599679744
3.6873-34.01732578870.2161430184911330.1786359149512504X-RAY DIFFRACTION99.5469988675

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