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- PDB-7shp: Crystal structure of hSTING in complex with c[2',3'-(ribo-2'-G, x... -

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Basic information

Entry
Database: PDB / ID: 7shp
TitleCrystal structure of hSTING in complex with c[2',3'-(ribo-2'-G, xylo-3'-A)-MP](RJ244)
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / STING / agonist / cGAMP analogs
Function / homology
Function and homology information


STING complex / STING mediated induction of host immune responses / 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 / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway ...STING complex / STING mediated induction of host immune responses / 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 / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / reticulophagy / cellular response to exogenous dsRNA / cellular response to organic cyclic compound / protein complex oligomerization / positive regulation of type I interferon production / positive regulation of macroautophagy / autophagosome membrane / autophagosome assembly / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / activation of innate immune response / antiviral innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of interferon-beta production / 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 / positive regulation of protein binding / peroxisome / 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-9UR / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXie, W. / Lama, L. / Yang, X.J. / Kuryavyi, V. / Nudelman, I. / Glickman, J.F. / Jones, R.A. / Tuschl, T. / Patel, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)AI141507 United States
CitationJournal: Cell Chem Biol / Year: 2023
Title: Arabinose- and xylose-modified analogs of 2',3'-cGAMP act as STING agonists.
Authors: Xie, W. / Lama, L. / Yang, X. / Kuryavyi, V. / Bhattacharya, S. / Nudelman, I. / Yang, G. / Ouerfelli, O. / Glickman, J.F. / Jones, R.A. / Tuschl, T. / Patel, D.J.
History
DepositionOct 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Refinement description / Category: 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
B: Stimulator of interferon genes protein
C: Stimulator of interferon genes protein
D: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4456
Polymers86,0974
Non-polymers1,3492
Water3,315184
1
A: Stimulator of interferon genes protein
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7233
Polymers43,0482
Non-polymers6741
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Stimulator of interferon genes protein
D: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7233
Polymers43,0482
Non-polymers6741
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.611, 131.109, 78.517
Angle α, β, γ (deg.)90.000, 92.080, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,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: 21524.158 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING1, ERIS, MITA, TMEM173 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86WV6
#2: Chemical ChemComp-9UR / (2S,5R,7R,8R,10S,12aR,14R,15R,15aR,16R)-7-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-14-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxyoctahydro-2H,10H,12H-5,8-methano-2lambda~5~,10lambda~5~-furo[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium formate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→29.92 Å / Num. obs: 37181 / % possible obs: 97.96 % / Redundancy: 4 % / Biso Wilson estimate: 35.44 Å2 / CC1/2: 0.975 / CC star: 0.994 / Rmerge(I) obs: 0.1293 / Rpim(I) all: 0.07236 / Rrim(I) all: 0.1485 / Net I/σ(I): 17.84
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4505 / Mean I/σ(I) obs: 5.74 / Num. unique obs: 3649 / CC1/2: 0.745 / CC star: 0.924 / Rpim(I) all: 0.07236 / Rrim(I) all: 0.1485 / % possible all: 96.48

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4loh

4loh


Resolution: 2.2→29.92 Å / SU ML: 0.3059 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.0455
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2509 1836 4.99 %
Rwork0.2073 34929 -
obs0.2094 36765 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 0 90 184 5940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415881
X-RAY DIFFRACTIONf_angle_d0.74527981
X-RAY DIFFRACTIONf_chiral_restr0.0447874
X-RAY DIFFRACTIONf_plane_restr0.00441030
X-RAY DIFFRACTIONf_dihedral_angle_d21.33932178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.37221350.30652657X-RAY DIFFRACTION96.24
2.26-2.330.34081120.28222657X-RAY DIFFRACTION96.85
2.33-2.40.32681420.24592664X-RAY DIFFRACTION98.08
2.4-2.490.26611350.23342701X-RAY DIFFRACTION98.47
2.49-2.590.28421480.22862691X-RAY DIFFRACTION97.56
2.59-2.70.28211320.22192684X-RAY DIFFRACTION99.4
2.7-2.850.3031620.23262740X-RAY DIFFRACTION99.18
2.85-3.020.3111550.22952690X-RAY DIFFRACTION98.96
3.02-3.260.28791270.21792698X-RAY DIFFRACTION98.67
3.26-3.580.2541580.20782672X-RAY DIFFRACTION98.16
3.59-4.10.22181680.18032651X-RAY DIFFRACTION97.11
4.1-5.160.18861340.16592722X-RAY DIFFRACTION98.69
5.16-29.920.20211280.19582702X-RAY DIFFRACTION96.92

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