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- PDB-7zv0: 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: 7zv0
TitleCrystal structure of human STING in complex with 3',3'-c-(2'F,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-K1C / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 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'F,2'dAMP)
Authors: Klima, M. / Smola, M. / Boura, E.
History
DepositionMay 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 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)23,8492
Polymers23,1891
Non-polymers6601
Water1,06359
1
A: Stimulator of interferon protein
hetero molecules

A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6994
Polymers46,3782
Non-polymers1,3212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4130 Å2
ΔGint-14 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.916, 110.916, 35.818
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
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-553-

HOH

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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-K1C / 9-[(1~{R},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{S})-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[13.3.0.0^{6,10}]octadecan-17-yl]purin-6-amine


Mass: 660.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24F2N10O9P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.31→34.08 Å / Num. obs: 10263 / % possible obs: 99.56 % / Redundancy: 9.5 % / Biso Wilson estimate: 29.16 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1526 / Rpim(I) all: 0.05162 / Rrim(I) all: 0.1614 / Net I/σ(I): 14.08
Reflection shellResolution: 2.31→2.393 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 983 / CC1/2: 0.801 / CC star: 0.943 / Rpim(I) all: 0.3036 / Rrim(I) all: 0.8729 / % possible all: 97.04

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Processing

Software
NameVersionClassification
XDSxdsgui2data reduction
XDSxdsgui2data scaling
PHASER2.8.3phasing
Coot0.9.6model building
PHENIX1.20_4459refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ksy

4ksy


Resolution: 2.31→34.08 Å / SU ML: 0.2559 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1026 10 %random selection
Rwork0.2059 9236 --
obs0.2083 10262 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.54 Å2
Refinement stepCycle: LAST / Resolution: 2.31→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 44 59 1463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171437
X-RAY DIFFRACTIONf_angle_d0.49991957
X-RAY DIFFRACTIONf_chiral_restr0.0378215
X-RAY DIFFRACTIONf_plane_restr0.0042250
X-RAY DIFFRACTIONf_dihedral_angle_d13.4951551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.430.30411400.25131263X-RAY DIFFRACTION97.5
2.43-2.580.25371440.23091296X-RAY DIFFRACTION99.93
2.58-2.780.28081440.22271288X-RAY DIFFRACTION100
2.78-3.060.27181450.21761305X-RAY DIFFRACTION100
3.06-3.510.24741460.20211318X-RAY DIFFRACTION99.93
3.51-4.410.19231500.17921346X-RAY DIFFRACTION100
4.42-34.080.19651570.20271420X-RAY DIFFRACTION99.56

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