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- PDB-4qxr: Crystal structure of hSTING(S162A/G230I/Q266I) in complex with DMXAA -

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Basic information

Entry
Database: PDB / ID: 4qxr
TitleCrystal structure of hSTING(S162A/G230I/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 / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / proton channel activity ...STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / serine/threonine protein kinase complex / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / proton channel activity / 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 / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / cytoplasmic vesicle membrane / Regulation of innate immune responses to cytosolic DNA / autophagosome / positive regulation of interferon-beta production / positive regulation of DNA-binding transcription factor activity / secretory granule membrane / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / peroxisome / regulation of inflammatory response / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / endosome / ciliary basal body / cilium / Golgi membrane / innate immune response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 / : / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / 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: 2.37 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)43,7975
Polymers43,1372
Non-polymers6613
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-25 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.576, 148.576, 36.202
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: 21568.340 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 155-341) / Mutation: S162A, G230I, 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.: 50 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 0.2 M Ca(Ac)2, 15% PEG3000, 0.1 M LiCl, 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: 2.37→128.671 Å / Num. all: 19048 / Num. obs: 19048 / % 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: 2.37→50 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 981 5.15 %RANDOM
Rwork0.187 ---
obs0.1893 19048 100 %-
all-19048 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 47 50 3025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073034
X-RAY DIFFRACTIONf_angle_d1.2034122
X-RAY DIFFRACTIONf_dihedral_angle_d18.3211138
X-RAY DIFFRACTIONf_chiral_restr0.075448
X-RAY DIFFRACTIONf_plane_restr0.004542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.49510.32741490.29162533X-RAY DIFFRACTION100
2.4951-2.65140.3881420.29222546X-RAY DIFFRACTION100
2.6514-2.85620.26681400.22932559X-RAY DIFFRACTION100
2.8562-3.14360.281350.20562551X-RAY DIFFRACTION100
3.1436-3.59850.20981360.17752587X-RAY DIFFRACTION100
3.5985-4.53380.18811460.15542593X-RAY DIFFRACTION100
4.5338-128.86060.21141330.17212698X-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)
14.625-3.35310.4686.8599-0.17592.9736-0.8048-0.9653-0.52311.36630.57960.16550.28730.24380.22320.41930.14430.08950.49610.15330.3419119.7412-45.6180.9079
23.599-3.63311.019.5628-0.55462.8698-0.06380.2429-0.80550.12320.2133-0.30.58320.3737-0.02490.42120.1380.03290.6459-0.05280.6367129.353-48.7083-7.1009
35.85866.4837-6.56239.3215-5.57588.1146-0.88691.2379-0.7595-0.41671.16810.61360.0975-1.4546-0.10670.43930.0322-0.01270.52810.11940.5919129.1486-52.5547-12.8258
47.5537-4.5153-2.22772.86091.04831.4922-0.9886-1.1618-1.81440.02030.24330.9635-0.013-0.04660.40120.7933-0.00410.23220.53520.11120.8596110.4692-51.7135-1.3574
53.6448-1.9552-0.04072.3155-0.11141.7574-0.102-0.0173-0.11250.11360.0133-0.15860.08270.22330.07220.3074-0.00780.010.30110.03030.2748124.754-41.4323-13.654
65.0093-2.542-0.42236.6833-1.04146.8768-0.3563-0.7204-0.0371.14160.4752-0.2161-0.6150.5594-0.10280.43070.0528-0.02320.4987-0.06910.3607123.364-32.6276-3.4192
77.4924-7.5601-2.54588.30973.96273.91341.07060.51150.7413-2.39310.2034-0.4202-1.4971.0416-1.11491.2099-0.0360.07661.09820.20921.0451136.1529-33.2184-19.3637
83.93160.7967-3.59769.94422.52934.3889-0.0798-1.56662.2980.16160.87160.0533-0.96881.3146-0.73720.4830.09840.00450.6805-0.19370.7524138.2183-41.3718-6.6489
95.0676.1333-0.31979.2284-1.20941.922-0.73880.8656-0.5878-0.78920.23460.40030.4546-0.30210.53530.379-0.0780.11930.4564-0.18080.4948102.7779-46.2422-15.6896
104.11773.0564-1.01442.1948-0.73384.0533-0.25290.1725-0.4022-0.950.4807-0.14111.0844-1.4521-0.16820.7926-0.26210.08330.809-0.02860.789389.4343-60.052-14.5866
113.24561.66320.03354.831-0.30023.60150.0959-0.1614-0.68660.3321-0.1757-0.16930.41770.16720.10940.3729-0.03170.05140.3587-0.00670.519994.8966-48.5955-2.3933
123.73663.03971.30742.50011.02410.78510.15340.8507-1.6972-0.40680.1129-0.7964-0.8144-0.0429-0.24440.7790.16480.16590.5122-0.1221.0026112.4208-51.6896-13.1983
133.3449-1.89331.81242.01650.89565.69170.4191.264-1.7916-0.2402-0.41220.0219-0.1884-0.42930.0260.3714-0.0192-0.01260.2747-0.09280.572285.9333-53.1198-4.2411
146.97164.8886-0.2253.5972-0.40210.3302-0.63070.1548-0.394-0.47350.4279-0.05220.1429-0.0110.10380.37410.0020.03680.3438-0.02190.505690.2196-50.514-6.8148
154.19383.50522.34697.90055.14777.049-0.0007-0.74260.17590.2832-0.1936-0.0761-0.2331-0.01770.20450.35750.04-0.00950.4111-0.01170.2047107.3523-32.31483.4381
165.4311-1.9276-1.73698.27575.95174.2934-0.0824-0.17430.1487-0.2388-0.31920.1127-0.9197-0.8060.21080.3660.02650.01580.32220.04730.327999.3068-29.463-6.9766
179.05830.9703-6.16334.4916-0.35514.0786-0.56551.7341-0.0968-0.93090.3457-0.05610.6964-1.2850.16750.571-0.0341-0.0190.57580.03080.377396.0561-40.1387-17.0384
189.54577.1404-0.75725.3768-0.69128.6160.9085-1.47521.28022.82520.2965-0.1022-1.14280.407-1.08720.93110.07150.12640.7813-0.24220.780885.7637-36.49035.1908
192.99692.43912.13749.0584-1.35562.931-0.3830.62420.6931-0.32550.22730.9659-0.6838-0.42010.07950.4372-0.02930.03740.44780.02030.527184.2902-43.4926-8.6366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 154:185)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 186:211)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 212:227)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 228:242)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 243:280)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 281:314)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 315:324)
8X-RAY DIFFRACTION8CHAIN A AND (RESID 325:335)
9X-RAY DIFFRACTION9CHAIN B AND (RESID 154:185)
10X-RAY DIFFRACTION10CHAIN B AND (RESID 186:197)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 198:227)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 228:242)
13X-RAY DIFFRACTION13CHAIN B AND (RESID 243:251)
14X-RAY DIFFRACTION14CHAIN B AND (RESID 252:262)
15X-RAY DIFFRACTION15CHAIN B AND (RESID 263:280)
16X-RAY DIFFRACTION16CHAIN B AND (RESID 281:300)
17X-RAY DIFFRACTION17CHAIN B AND (RESID 301:314)
18X-RAY DIFFRACTION18CHAIN B AND (RESID 315:324)
19X-RAY DIFFRACTION19CHAIN B AND (RESID 325:335)

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