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- PDB-5bqx: Crystal structure of human STING in complex with 3'2'-cGAMP -

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Basic information

Entry
Database: PDB / ID: 5bqx
TitleCrystal structure of human STING in complex with 3'2'-cGAMP
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / STING / 3'2'-cGAMP
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / proton channel activity / 2',3'-cyclic GMP-AMP binding / STING mediated induction of host immune responses / cyclic-di-GMP binding / 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 / proton channel activity / 2',3'-cyclic GMP-AMP binding / STING mediated induction of host immune responses / cyclic-di-GMP binding / 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 / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / cellular response to organic cyclic compound / autophagosome assembly / autophagosome / positive regulation of type I interferon production / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / positive regulation of interferon-beta production / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / cytoplasmic vesicle membrane / positive regulation of DNA-binding transcription factor activity / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein complex oligomerization / 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
3'2'-cGAMP / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsWu, J. / Zhang, X. / Chen, Z.J. / Chen, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1-GM-079554 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1-AI-093967 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Molecular basis for the specific recognition of the metazoan cyclic GMP-AMP by the innate immune adaptor protein STING.
Authors: Shi, H. / Wu, J. / Chen, Z.J. / Chen, C.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water1,62190
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 operation8_554-y,-x,-z-1/21
Buried area4320 Å2
ΔGint-18 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.061, 111.061, 35.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-574-

HOH

21A-590-

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
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-4UR / 3'2'-cGAMP / 2-amino-9-[(2S,5R,7R,8R,10R,12aR,14R,15R,15aS,16R)-7-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxidooctahydro-12H-5,8-methanofuro[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-14-yl]-1,9-dihydro-6H-purin-6-one


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.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.2 M ammonium acetate, 0.1 M trisodium citrate, pH 5.8, 25% PEG4000

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 15799 / % possible obs: 100 % / Redundancy: 13.6 % / Net I/σ(I): 27.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2→49.668 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 1553 10 %
Rwork0.1868 --
obs0.1908 15528 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→49.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 45 90 1576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081529
X-RAY DIFFRACTIONf_angle_d1.0392083
X-RAY DIFFRACTIONf_dihedral_angle_d15.337575
X-RAY DIFFRACTIONf_chiral_restr0.043225
X-RAY DIFFRACTIONf_plane_restr0.005268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9997-2.06420.30921400.24861257X-RAY DIFFRACTION100
2.0642-2.1380.26141400.23621257X-RAY DIFFRACTION100
2.138-2.22360.2751370.23451235X-RAY DIFFRACTION98
2.2236-2.32480.46111190.36281096X-RAY DIFFRACTION86
2.3248-2.44740.23581400.19841265X-RAY DIFFRACTION100
2.4474-2.60070.23861420.18711278X-RAY DIFFRACTION100
2.6007-2.80150.21831420.18561278X-RAY DIFFRACTION100
2.8015-3.08340.22251440.18111292X-RAY DIFFRACTION100
3.0834-3.52950.20051440.1721294X-RAY DIFFRACTION100
3.5295-4.44630.21851480.15291321X-RAY DIFFRACTION100
4.4463-49.68330.19111570.17471402X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.54493.0825-1.14889.0660.57848.24880.07830.06650.5448-0.1737-0.04870.6057-0.5518-0.9642-0.02590.26050.0441-0.00990.29610.01760.2084-24.54829.9065-5.2153
24.2138-4.5780.24166.15651.02772.0747-0.0785-1.8692-0.08970.78810.048-0.72180.43450.8291-0.03080.35570.0273-0.10520.62190.19730.4105-5.037120.16822.3799
37.37960.60260.49851.72341.93196.43980.1014-0.2414-0.32630.02320.032-0.48940.55680.7245-0.10420.3129-0.0381-0.01940.35860.06550.4133-5.050528.5992-8.6017
48.68884.766-0.75913.5445-0.26051.0881-0.15010.2672-0.48560.0280.0873-0.36460.03160.14150.07250.26440.03280.00160.35-0.00280.3037-3.990422.9537-9.5024
53.7749-1.51665.19343.2543-1.18167.66440.20480.0878-0.06990.0878-0.07150.25950.2664-0.0171-0.24610.3319-0.02540.01620.3384-0.02030.2252-25.211330.0955-19.4102
65.5882-1.47514.48347.9724-5.16695.3819-0.2492-0.40520.57060.205-0.22190.0326-0.9052-0.5740.56230.28970.0070.00510.2173-0.05080.2838-21.51937.9823-8.4443
77.91260.7368-0.53015.95661.02072.12790.5037-0.32830.81140.7015-0.27390.0233-0.88671.3165-0.04690.346-0.1446-0.02540.473-0.04120.4246-9.521835.822-5.3282
83.9559-0.08914.98396.01191.06538.0313-0.4252-0.84682.3751.4903-0.04950.5921-0.1045-0.47870.44570.3424-0.06460.08260.5024-0.10390.7109-0.230638.3257-6.6905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 152 through 167 )
2X-RAY DIFFRACTION2chain 'A' and (resid 168 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 211 )
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 262 )
5X-RAY DIFFRACTION5chain 'A' and (resid 263 through 280 )
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 301 )
7X-RAY DIFFRACTION7chain 'A' and (resid 302 through 324 )
8X-RAY DIFFRACTION8chain 'A' and (resid 325 through 336 )

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