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- PDB-8orw: Crystal structure of human STING in complex with the agonist MD1203 -

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Basic information

Entry
Database: PDB / ID: 8orw
TitleCrystal structure of human STING in complex with the agonist MD1203
ComponentsStimulator of interferon protein
KeywordsANTIVIRAL PROTEIN / sting / antiviral / activator
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-VZ6 / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsKlima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Fluorinated cGAMP analogs, which act as STING agonists and are not cleavable by poxins: Structural basis of their function.
Authors: Klima, M. / Dejmek, M. / Duchoslav, V. / Eisenreichova, A. / Sala, M. / Chalupsky, K. / Chalupska, D. / Novotna, B. / Birkus, G. / Nencka, R. / Boura, E.
History
DepositionApr 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: 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 1.2Apr 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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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)23,8502
Polymers23,1891
Non-polymers6611
Water00
1
A: Stimulator of interferon protein
hetero molecules

A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7014
Polymers46,3782
Non-polymers1,3232
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3970 Å2
ΔGint-17 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.442, 78.145, 35.937
Angle α, β, γ (deg.)90.000, 97.440, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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 BL21(DE3) (bacteria) / References: UniProt: A0A2R3XZB7
#2: Chemical ChemComp-VZ6 / 9-[(1~{S},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one


Mass: 661.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23F2N9O10P2 / Feature type: SUBJECT OF INVESTIGATION
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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 8.000; 200 mM lithium chloride; 100 mM Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.95→44.34 Å / Num. obs: 4988 / % possible obs: 95.11 % / Redundancy: 6.4 % / Biso Wilson estimate: 75.27 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.3852 / Rpim(I) all: 0.161 / Rrim(I) all: 0.4183 / Net I/σ(I): 6.43
Reflection shellResolution: 2.95→3.055 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.025 / Mean I/σ(I) obs: 0.77 / Num. unique obs: 494 / CC1/2: 0.455 / CC star: 0.791 / Rpim(I) all: 0.8413 / Rrim(I) all: 2.197 / % possible all: 93.23

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Processing

Software
NameVersionClassification
XDSxdsapp 3.1.9data reduction
XDSxdsapp 3.1.9data scaling
PHASER2.8.3phasing
Coot0.9.8.7model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→44.34 Å / SU ML: 0.3731 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2168
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 248 4.98 %random selection
Rwork0.2189 4727 --
obs0.2205 4975 95.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.01 Å2
Refinement stepCycle: LAST / Resolution: 2.95→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 44 0 1457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021487
X-RAY DIFFRACTIONf_angle_d0.52942022
X-RAY DIFFRACTIONf_chiral_restr0.0395222
X-RAY DIFFRACTIONf_plane_restr0.0032268
X-RAY DIFFRACTIONf_dihedral_angle_d11.9299586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.720.31961240.26662335X-RAY DIFFRACTION94.61
3.72-44.340.22331240.20072392X-RAY DIFFRACTION95.67

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