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- PDB-4qxq: Crystal structure of hSTING(S162A/Q266I) in complex with DMXAA -

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Basic information

Entry
Database: PDB / ID: 4qxq
TitleCrystal structure of hSTING(S162A/Q266I) in complex with DMXAA
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / innate immunity / cGAMP Binding / Membrane
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
(5,6-dimethyl-9-oxo-9H-xanthen-4-yl)acetic acid / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsGao, P. / Patel, D.J.
CitationJournal: Cell Rep / Year: 2014
Title: Binding-Pocket and Lid-Region Substitutions Render Human STING Sensitive to the Species-Specific Drug DMXAA.
Authors: Gao, P. / Zillinger, T. / Wang, W. / Ascano, M. / Dai, P. / Hartmann, G. / Tuschl, T. / Deng, L. / Barchet, W. / Patel, D.J.
History
DepositionJul 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Downloads & links

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Assembly

Deposited unit
A: Stimulator of interferon genes protein
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6855
Polymers43,0242
Non-polymers6613
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-25 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.954, 147.954, 36.122
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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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: 21512.234 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 155-341) / Mutation: S162A, H232R, Q266I
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-1YE / (5,6-dimethyl-9-oxo-9H-xanthen-4-yl)acetic acid


Mass: 282.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 0.2 M Ca(Ac)2, 15% PEG3000, 0.01 M L-Proline, 0.1 M NaAc, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.55 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.42→128.132 Å / Num. all: 17687 / Num. obs: 17687 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
RAPDdata reduction
RAPDdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→50 Å / SU ML: 0.36 / σ(F): 1.37 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 900 5.09 %RANDOM
Rwork0.1826 ---
obs0.1849 17687 99.92 %-
all-17687 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 47 64 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143030
X-RAY DIFFRACTIONf_angle_d1.6134116
X-RAY DIFFRACTIONf_dihedral_angle_d19.5671134
X-RAY DIFFRACTIONf_chiral_restr0.094444
X-RAY DIFFRACTIONf_plane_restr0.006542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.57170.38131510.32092749X-RAY DIFFRACTION100
2.5717-2.77030.29561240.25082785X-RAY DIFFRACTION100
2.7703-3.04910.25721630.21252762X-RAY DIFFRACTION100
3.0491-3.49040.23931520.17842768X-RAY DIFFRACTION100
3.4904-4.39750.18921570.15162807X-RAY DIFFRACTION100
4.3975-128.31180.20931530.16662916X-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)
15.9722-1.1178-0.38221.33490.20161.75680.21280.9436-0.0733-0.3067-0.3874-0.1726-0.04680.16170.18830.25340.07350.07550.31030.08180.2519172.72147.3865-5.866
20.63280.9561-1.12381.455-1.70241.99660.22362.50990.48770.32430.4937-0.6010.40140.9611-0.3780.34330.06250.01450.7278-0.18840.9942190.798442.0205-3.5854
35.78951.5375-1.12853.3168-0.39834.01960.2141-1.2485-0.38780.49350.0116-0.06760.02210.3522-0.05480.2740.0404-0.0470.45440.07140.404170.708839.76537.4402
41.44670.34580.89447.9564-3.19192.3372-0.2837-0.09880.19040.63460.1878-0.8066-0.67480.1563-0.03330.4807-0.08330.00090.3883-0.00420.4005183.475640.920810.1738
52.4041-1.6704-0.65791.14610.40711.207-0.08710.22810.3173-0.0231-0.0117-0.3709-0.02170.0440.03480.2443-0.0185-0.0020.27040.02990.3434172.842446.4354.7085
64.67750.9648-3.43622.9261-1.51272.9523-0.3680.2443-0.47110.1364-0.057-0.30940.9835-0.66840.36250.3605-0.0224-0.07330.3488-0.05960.2887158.808737.12742.4555
75.8148-0.50640.32363.1473-1.42447.20830.51281.6665-0.3026-0.71580.08370.16670.4492-0.0973-0.34370.5190.064-0.09260.6208-0.06040.44170.256238.6578-7.1494
87.5278-3.5637-3.71981.6871.74989.81410.0458-2.027-1.43291.337-0.02391.79062.43610.3927-0.14441.2692-0.07440.10420.69240.26041.1103170.627627.341514.5534
99.0488-5.04522.04943.3618-2.39993.41680.23040.952-0.912-0.7421-0.49661.99281.4968-0.7976-0.12780.4443-0.014-0.06480.4647-0.040.6744178.503429.51172.0047
101.18151.2374-0.98985.4982-2.27451.28850.1075-0.04590.15790.277-0.1307-0.1873-0.25850.12170.04290.3109-0.005-0.03420.2744-0.0250.2894164.578368.61375.2563
111.57530.3661-0.3174.4695-0.10730.97590.0602-0.23720.04590.2045-0.0996-0.32660.0274-0.00580.06860.26750.0012-0.03090.34430.00410.2681159.742261.6690.7515
123.54630.1756-0.69826.1072-1.5252.9035-0.0905-0.1850.21650.21760.01140.3911-0.4021-0.26210.09310.30160.0023-0.02310.2782-0.0370.3329153.194871.0163.256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 154:185)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 186:197)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 198:211)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 212:224)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 225:280)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 281:300)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 301:314)
8X-RAY DIFFRACTION8CHAIN A AND (RESID 315:324)
9X-RAY DIFFRACTION9CHAIN A AND (RESID 325:335)
10X-RAY DIFFRACTION10CHAIN B AND (RESID 154:224)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 225:300)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 301:335)

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