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- PDB-8ydn: Crystal structure of a STING from C. gigas in complex with c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 8ydn
TitleCrystal structure of a STING from C. gigas in complex with c-di-GMP
ComponentsStimulator of interferon genes protein
KeywordsANTIVIRAL PROTEIN / complex
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / autophagosome / innate immune response / endoplasmic reticulum membrane
Similarity search - Function
: / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain
Similarity search - Domain/homology
Chem-C2E / STING ligand-binding domain-containing protein
Similarity search - Component
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsZhang, Y. / Yu, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of TM-STING C-terminal domain from the Pacific Oyster Crassostrea gigas
Authors: Zhang, Y. / Yu, F.
History
DepositionFeb 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: 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 genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7372
Polymers40,0471
Non-polymers6901
Water00
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4754
Polymers80,0942
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y,-z+3/41
Buried area4280 Å2
ΔGint-12 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.400, 104.400, 96.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Stimulator of interferon genes protein


Mass: 40046.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: CGI_10003079 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(codon plus) / References: UniProt: K1QMA0
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 1.65 Å3/Da / Density % sol: 25.32 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% PEG 400, 0.1 M MES pH 6.5, 2.0 M ammonium sulfate
PH range: 6.5-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.04→70.99 Å / Num. obs: 17362 / % possible obs: 99.68 % / Redundancy: 25 % / Biso Wilson estimate: 38.04 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1871 / Rpim(I) all: 0.03825 / Rrim(I) all: 0.1911 / Net I/σ(I): 21.38
Reflection shellResolution: 2.04→2.09 Å / Num. unique obs: 1278 / CC1/2: 0.758 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→70.99 Å / SU ML: 0.3055 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2675 874 5.05 %
Rwork0.2325 16436 -
obs0.2341 17310 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.06 Å2
Refinement stepCycle: LAST / Resolution: 2.04→70.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 24 0 1526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221567
X-RAY DIFFRACTIONf_angle_d1.54372123
X-RAY DIFFRACTIONf_chiral_restr0.0712234
X-RAY DIFFRACTIONf_plane_restr0.0094267
X-RAY DIFFRACTIONf_dihedral_angle_d14.2904215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.170.35761490.29112685X-RAY DIFFRACTION99.61
2.17-2.340.29761700.28722662X-RAY DIFFRACTION99.4
2.34-2.570.32731620.28672678X-RAY DIFFRACTION99.58
2.57-2.940.33561500.27742718X-RAY DIFFRACTION99.76
2.94-3.710.26691220.23042780X-RAY DIFFRACTION99.86
3.71-70.990.19461210.1932913X-RAY DIFFRACTION99.93

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