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

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Basic information

Entry
Database: PDB / ID: 7zku
TitleCrystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP-2'dGMP)
ComponentsStimulator of interferon protein
KeywordsANTIVIRAL PROTEIN / sting / antiviral / activator
Function / homology
Function and homology information


autophagosome membrane / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / mitochondrial outer membrane / nucleotide binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm
Similarity search - Function
: / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain
Similarity search - Domain/homology
Chem-JLU / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKlima, M. / Smola, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human STING in complex with 3',3'-c-(2'F,2'dAMP-2'dGMP)
Authors: Klima, M. / Smola, M. / Boura, E.
History
DepositionApr 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stimulator of interferon protein
B: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers46,3782
Non-polymers6581
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-18 kcal/mol
Surface area16930 Å2
Unit cell
Length a, b, c (Å)93.158, 93.158, 204.062
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Stimulator of interferon protein


Mass: 23189.064 Da / Num. of mol.: 2
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-JLU / 9-[(1~{S},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R})-8-(6-aminopurin-9-yl)-9-fluoranyl-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-17-yl]-2-azanyl-3~{H}-purin-6-one


Mass: 658.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25FN10O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.98 Å3/Da / Density % sol: 58.66 %
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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→15.94 Å / Num. obs: 58210 / % possible obs: 99.8 % / Redundancy: 22.8 % / Biso Wilson estimate: 29.79 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.03036 / Rrim(I) all: 0.1462 / Net I/σ(I): 16.01
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 23.3 % / Rmerge(I) obs: 4.412 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 5703 / CC1/2: 0.307 / CC star: 0.686 / Rpim(I) all: 0.9209 / Rrim(I) all: 4.509 / % possible all: 99.95

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Processing

Software
NameVersionClassification
XDSxdsapp 2.0data reduction
XDSxdsapp 2.0data scaling
PHASER2.8.3phasing
Coot0.9.6model building
PHENIX1.20_4459refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ksy

4ksy


Resolution: 1.7→15.94 Å / SU ML: 0.2249 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 2910 5 %random selection
Rwork0.2218 55292 --
obs0.2229 58202 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.37 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 44 226 3283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493196
X-RAY DIFFRACTIONf_angle_d0.73554358
X-RAY DIFFRACTIONf_chiral_restr0.0455475
X-RAY DIFFRACTIONf_plane_restr0.0069563
X-RAY DIFFRACTIONf_dihedral_angle_d13.93131226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.33561360.33552583X-RAY DIFFRACTION99.96
1.73-1.760.33821360.32472594X-RAY DIFFRACTION99.93
1.76-1.790.30811360.31332566X-RAY DIFFRACTION99.96
1.79-1.820.34061360.30542586X-RAY DIFFRACTION99.96
1.82-1.860.31051360.2852581X-RAY DIFFRACTION100
1.86-1.90.32321360.30432596X-RAY DIFFRACTION100
1.9-1.950.30471360.26562593X-RAY DIFFRACTION100
1.95-1.990.28851360.25232585X-RAY DIFFRACTION100
1.99-2.050.23891370.2382598X-RAY DIFFRACTION100
2.05-2.110.27111360.23982602X-RAY DIFFRACTION99.96
2.11-2.180.28161380.23192618X-RAY DIFFRACTION100
2.18-2.250.26491370.22582606X-RAY DIFFRACTION100
2.25-2.340.29121380.22742625X-RAY DIFFRACTION99.96
2.34-2.450.27651390.22492626X-RAY DIFFRACTION100
2.45-2.580.23461380.22632629X-RAY DIFFRACTION100
2.58-2.740.22211410.21462659X-RAY DIFFRACTION100
2.74-2.950.22561380.2242632X-RAY DIFFRACTION100
2.95-3.240.24661410.21532684X-RAY DIFFRACTION99.96
3.24-3.710.2221410.20572684X-RAY DIFFRACTION100
3.71-4.650.21491440.1872748X-RAY DIFFRACTION99.9
4.65-15.940.22691540.21462897X-RAY DIFFRACTION100

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