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- PDB-7ssm: Crystal structure of human STING R232 in complex with compound 11 -

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Basic information

Entry
Database: PDB / ID: 7ssm
TitleCrystal structure of human STING R232 in complex with compound 11
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / RECEPTOR
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle ...2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm
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-B7L / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSack, J.S. / Critton, D.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of Non-Nucleotide Small-Molecule STING Agonists via Chemotype Hybridization.
Authors: Cherney, E.C. / Zhang, L. / Lo, J. / Huynh, T. / Wei, D. / Ahuja, V. / Quesnelle, C. / Schieven, G.L. / Futran, A. / Locke, G.A. / Lin, Z. / Monereau, L. / Chaudhry, C. / Blum, J. / Li, S. / ...Authors: Cherney, E.C. / Zhang, L. / Lo, J. / Huynh, T. / Wei, D. / Ahuja, V. / Quesnelle, C. / Schieven, G.L. / Futran, A. / Locke, G.A. / Lin, Z. / Monereau, L. / Chaudhry, C. / Blum, J. / Li, S. / Fereshteh, M. / Li-Wang, B. / Gangwar, S. / Pan, C. / Chong, C. / Zhu, X. / Posy, S.L. / Sack, J.S. / Zhang, P. / Ruzanov, M. / Harner, M. / Akhtar, F. / Schroeder, G.M. / Vite, G. / Fink, B.
History
DepositionNov 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 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.title / _citation.year / _citation_author.name
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 18, 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)24,3902
Polymers24,0541
Non-polymers3361
Water68538
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7804
Polymers48,1082
Non-polymers6732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3620 Å2
ΔGint-17 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.080, 110.080, 36.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Stimulator of interferon genes protein / Transmembrane protein 173


Mass: 24053.945 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
#2: Chemical ChemComp-B7L / 2-({[(8R)-pyrazolo[1,5-a]pyrimidine-3-carbonyl]amino}methyl)-1-benzofuran-7-carboxylic acid


Mass: 336.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2 M Na/K tartrate, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→77.84 Å / Num. obs: 13213 / % possible obs: 80.4 % / Redundancy: 12.6 % / Biso Wilson estimate: 39.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Net I/σ(I): 15.5
Reflection shellResolution: 1.96→2.12 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.709 / Mean I/σ(I) obs: 1.4 / Num. measured all: 1303 / Num. unique obs: 109 / CC1/2: 0.717 / Rpim(I) all: 0.408 / Rrim(I) all: 1.456 / Net I/σ(I) obs: 1.6 / % possible all: 19.9

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F5Y

4f5y


Resolution: 1.96→49.23 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.187 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.25 673 5.09 %RANDOM
Rwork0.207 ---
obs0.209 13213 79.7 %-
Displacement parametersBiso max: 112.5 Å2 / Biso mean: 43.78 Å2 / Biso min: 23.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.2708 Å20 Å20 Å2
2---0.2708 Å20 Å2
3---0.5416 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 1.96→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 25 38 1356
Biso mean--34.56 47.24 -
Num. residues----169
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d446SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes267HARMONIC5
X-RAY DIFFRACTIONt_it1361HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion177SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1530SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1361HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1864HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion17.81
LS refinement shellResolution: 1.96→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 33
RfactorNum. reflection% reflection
Rfree0.1833 19 4.74 %
Rwork0.2218 382 -
all0.22 401 -
obs--13.2 %

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