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- PDB-7zxb: Crystal structure of human STING in complex with 3',3'-c-(2'dAMP-... -

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Basic information

Entry
Database: PDB / ID: 7zxb
TitleCrystal structure of human STING in complex with 3',3'-c-(2'dAMP-2'F,2'dAMP)
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-KAX / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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'dAMP-2'F,2'dAMP)
Authors: Klima, M. / Smola, M. / Boura, E.
History
DepositionMay 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8312
Polymers23,1891
Non-polymers6421
Water00
1
A: Stimulator of interferon protein
hetero molecules

A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6634
Polymers46,3782
Non-polymers1,2852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4210 Å2
ΔGint-12 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.803, 111.803, 35.115
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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

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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-KAX / 9-[(1~{R},6~{R},8~{R},10~{S},15~{R},17~{R},18~{S})-8-(6-aminopurin-9-yl)-18-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]purin-6-amine


Mass: 642.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25FN10O9P2 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
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: Feb 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3→35.36 Å / Num. obs: 4804 / % possible obs: 99.61 % / Redundancy: 16.2 % / Biso Wilson estimate: 71.06 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1612 / Rpim(I) all: 0.04082 / Rrim(I) all: 0.1665 / Net I/σ(I): 17.29
Reflection shellResolution: 3→3.107 Å / Redundancy: 17.3 % / Rmerge(I) obs: 1.256 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 465 / CC1/2: 0.806 / CC star: 0.945 / Rpim(I) all: 0.3076 / Rrim(I) all: 1.294 / % possible all: 100

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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: 3→35.36 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.8023
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 241 5.02 %random selection
Rwork0.2322 8082 --
obs0.2342 4804 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.3 Å2
Refinement stepCycle: LAST / Resolution: 3→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 43 0 1443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241474
X-RAY DIFFRACTIONf_angle_d0.51482006
X-RAY DIFFRACTIONf_chiral_restr0.041220
X-RAY DIFFRACTIONf_plane_restr0.0034256
X-RAY DIFFRACTIONf_dihedral_angle_d12.9225553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.430.36831470.31562699X-RAY DIFFRACTION99.86
3.43-4.320.29461350.23952702X-RAY DIFFRACTION100
4.32-35.360.22511450.19962681X-RAY DIFFRACTION99.3

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