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

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Basic information

Entry
Database: PDB / ID: 7zwl
TitleCrystal structure of human STING in complex with 3',3'-c-di-(2'F,2'dAMP)
Components
  • Stimulator of interferon protein
  • Ubiquitin-like protein SMT3
KeywordsANTIVIRAL PROTEIN / sting / antiviral / activator
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / positive regulation of type I interferon production / autophagosome membrane / protein sumoylation / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / condensed nuclear chromosome / protein tag activity / monoatomic ion transmembrane transport / cytoplasmic vesicle / mitochondrial outer membrane / Golgi membrane / nucleotide binding / perinuclear region of cytoplasm / identical protein binding / nucleus
Similarity search - Function
: / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-K43 / Stimulator of interferon genes protein / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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-di-(2'F,2'dAMP)
Authors: Klima, M. / Smola, M. / Boura, E.
History
DepositionMay 19, 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
B: Stimulator of interferon protein
C: Ubiquitin-like protein SMT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2414
Polymers57,5833
Non-polymers6581
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-17 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.969, 92.969, 203.905
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
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

21A-584-

HOH

31B-471-

HOH

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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: Protein Ubiquitin-like protein SMT3


Mass: 11204.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12306
#3: Chemical ChemComp-K43 / 9-[(1~{R},6~{R},8~{R},9~{S},10~{R},15~{R},17~{R},18~{S})-17-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,11,13-tetraoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]purin-6-amine / 3',3'-c-di-(2'F,2'dAMP)


Mass: 658.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26F2N10O8P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
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: 2→15.96 Å / Num. obs: 35943 / % possible obs: 99.69 % / Redundancy: 22.7 % / Biso Wilson estimate: 33.8 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.2265 / Rpim(I) all: 0.04809 / Rrim(I) all: 0.2316 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.071 Å / Redundancy: 22.9 % / Rmerge(I) obs: 3.083 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 3515 / CC1/2: 0.438 / CC star: 0.781 / Rpim(I) all: 0.653 / Rrim(I) all: 3.152 / % 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: 2→15.96 Å / SU ML: 0.2546 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4384
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 1795 4.99 %random selection
Rwork0.2163 34142 --
obs0.2179 35937 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.08 Å2
Refinement stepCycle: LAST / Resolution: 2→15.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 44 162 3731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00593651
X-RAY DIFFRACTIONf_angle_d0.76434952
X-RAY DIFFRACTIONf_chiral_restr0.0446539
X-RAY DIFFRACTIONf_plane_restr0.0071654
X-RAY DIFFRACTIONf_dihedral_angle_d13.29881396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33251350.32322551X-RAY DIFFRACTION99.89
2.05-2.110.36781350.30042580X-RAY DIFFRACTION99.89
2.11-2.180.27951340.27332555X-RAY DIFFRACTION100
2.18-2.260.30221370.24942593X-RAY DIFFRACTION99.96
2.26-2.350.26751350.24632577X-RAY DIFFRACTION99.96
2.35-2.460.29431360.24182586X-RAY DIFFRACTION99.93
2.46-2.590.30571380.23812607X-RAY DIFFRACTION100
2.59-2.750.26731370.2322599X-RAY DIFFRACTION100
2.75-2.960.30381370.23032625X-RAY DIFFRACTION100
2.96-3.250.28021390.22792629X-RAY DIFFRACTION100
3.25-3.720.22421410.20972673X-RAY DIFFRACTION100
3.72-4.670.22081410.17052705X-RAY DIFFRACTION100
4.67-15.960.18681500.19232862X-RAY DIFFRACTION99.97

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