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- PDB-4ksy: Crystal structure of STING in complex with cGAMP -

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Basic information

Entry
Database: PDB / ID: 4ksy
TitleCrystal structure of STING in complex with cGAMP
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / innate immunity
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / reticulophagy / pattern recognition receptor signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / protein complex oligomerization / positive regulation of macroautophagy / autophagosome membrane / cellular response to organic cyclic compound / autophagosome assembly / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / antiviral innate immune response / activation of innate immune response / positive regulation of interferon-beta production / endoplasmic reticulum-Golgi intermediate compartment membrane / autophagosome / Regulation of innate immune responses to cytosolic DNA / secretory granule membrane / positive regulation of DNA-binding transcription factor activity / cytoplasmic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / peroxisome / positive regulation of protein binding / regulation of inflammatory response / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
cGAMP / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.881 Å
AuthorsZhang, X. / Chen, Z.J. / Zhang, X.W.
CitationJournal: Mol.Cell / Year: 2013
Title: Cyclic GMP-AMP Containing Mixed Phosphodiester Linkages Is An Endogenous High-Affinity Ligand for STING.
Authors: Zhang, X. / Shi, H. / Wu, J. / Zhang, X. / Sun, L. / Chen, C. / Chen, Z.J.
History
DepositionMay 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Aug 5, 2015Group: Non-polymer description
Revision 1.4Jun 27, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)27,8552
Polymers27,1811
Non-polymers6741
Water1,29772
1
A: Stimulator of interferon genes protein
hetero molecules

A: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7104
Polymers54,3612
Non-polymers1,3492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area3870 Å2
ΔGint-15 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.522, 77.927, 35.974
Angle α, β, γ (deg.)90.00, 96.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

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Components

#1: Protein Stimulator of interferon genes protein / hSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / hMITA / ...hSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / hMITA / Transmembrane protein 173


Mass: 27180.645 Da / Num. of mol.: 1 / Fragment: UNP residues 138-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM173, ERIS, MITA, STING / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WV6
#2: Chemical ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O13P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.8
Details: 27% PEG 3,350, 0.1 M Bis-Tris, pH 6.8, 0.2 M NaCl, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 19800 / % possible obs: 99.4 % / Observed criterion σ(F): -3
Reflection shellResolution: 1.88→1.91 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.881→29.461 Å / SU ML: 0.18 / σ(F): 1.38 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 1980 10 %
Rwork0.1607 --
obs0.1629 19800 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.881→29.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 45 72 1582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071565
X-RAY DIFFRACTIONf_angle_d1.2132136
X-RAY DIFFRACTIONf_dihedral_angle_d15.316591
X-RAY DIFFRACTIONf_chiral_restr0.077232
X-RAY DIFFRACTIONf_plane_restr0.005276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8813-1.92830.31651370.24191227X-RAY DIFFRACTION97
1.9283-1.98050.23631390.19431259X-RAY DIFFRACTION99
1.9805-2.03870.20531410.1771262X-RAY DIFFRACTION99
2.0387-2.10450.21411400.17281268X-RAY DIFFRACTION99
2.1045-2.17970.18351400.16411252X-RAY DIFFRACTION99
2.1797-2.26690.15921420.1591279X-RAY DIFFRACTION99
2.2669-2.37010.19621420.15441286X-RAY DIFFRACTION99
2.3701-2.4950.19041410.16471266X-RAY DIFFRACTION100
2.495-2.65120.2031390.16411257X-RAY DIFFRACTION100
2.6512-2.85570.17991430.16611287X-RAY DIFFRACTION100
2.8557-3.14280.18911440.16431286X-RAY DIFFRACTION100
3.1428-3.59690.15931430.16151293X-RAY DIFFRACTION100
3.5969-4.52910.15551430.14041288X-RAY DIFFRACTION100
4.5291-29.46450.1881460.16011310X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 34.5257 Å / Origin y: 5.8054 Å / Origin z: -18.3776 Å
111213212223313233
T0.1783 Å20.0185 Å2-0.0045 Å2-0.22 Å20.0088 Å2--0.2155 Å2
L1.612 °2-0.0312 °20.0162 °2-1.9156 °20.1445 °2--1.5863 °2
S-0.0428 Å °0.0107 Å °0.1516 Å °-0.0458 Å °0.0188 Å °0.2426 Å °0.0446 Å °-0.2678 Å °-0.002 Å °
Refinement TLS groupSelection details: all

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