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- PDB-4qxp: Crystal structure of hSTING(G230I) in complex with DMXAA -

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Basic information

Entry
Database: PDB / ID: 4qxp
TitleCrystal structure of hSTING(G230I) 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 / proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / cGAS/STING signaling pathway / 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 / proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / cGAS/STING signaling pathway / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / reticulophagy / pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / autophagosome assembly / cellular response to organic cyclic compound / 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 / positive regulation of interferon-beta production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / cytoplasmic vesicle membrane / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / protein complex oligomerization / positive regulation of protein binding / regulation of inflammatory response / defense response to virus / mitochondrial outer membrane / RNA polymerase II-specific DNA-binding transcription factor binding / 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: 2.51 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)43,7634
Polymers43,1992
Non-polymers5652
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-15 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.570, 77.919, 79.634
Angle α, β, γ (deg.)90.00, 98.97, 90.00
Int Tables number4
Space group name H-MP1211

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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: 21599.311 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 155-341) / Mutation: G230I, H232R
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 / Vadimezan


Mass: 282.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14O4
#3: Water ChemComp-HOH / water / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.2 M Li2SO4, 20% PEG 3350, 0.015 mM CYMAL-7, 0.1 M Tris, pH 8.1, 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: 2.51→78.66 Å / Num. all: 15137 / Num. obs: 14320 / % possible obs: 94.6 % / 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: 2.51→50 Å / SU ML: 0.38 / σ(F): 1.39 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 720 5.03 %RANDOM
Rwork0.1975 ---
obs0.1995 14320 94.13 %-
all-15137 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 42 50 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073034
X-RAY DIFFRACTIONf_angle_d1.2624120
X-RAY DIFFRACTIONf_dihedral_angle_d20.4461142
X-RAY DIFFRACTIONf_chiral_restr0.081446
X-RAY DIFFRACTIONf_plane_restr0.005544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.7040.33561450.29062650X-RAY DIFFRACTION92
2.704-2.97610.32011560.26152706X-RAY DIFFRACTION94
2.9761-3.40680.29151490.22662678X-RAY DIFFRACTION93
3.4068-4.29210.22611230.18042763X-RAY DIFFRACTION95
4.2921-78.69850.19291470.17052803X-RAY DIFFRACTION95
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)
10.5884-0.38080.04923.24361.39811.0127-0.0732-0.16290.0759-0.20780.5745-0.89230.510.4198-0.25510.43930.0825-0.05640.3018-0.06480.439818.5649-84.9417-65.0832
21.3482-0.39290.55083.57370.11181.1882-0.17540.1904-0.9845-0.1476-0.0773-0.95030.5475-0.15930.26620.44440.07750.10630.4429-0.13460.794215.0533-97.1915-72.8326
30.3197-0.7523-0.27152.38471.70581.9616-0.1620.0679-1.4908-0.4128-0.46862.4070.1596-0.07630.31380.41340.0870.00150.53520.03521.1526-0.0262-86.621-74.0738
42.334-1.2271-1.04134.14610.02384.4152-0.128-0.6561-0.21751.09920.2608-0.29510.3088-0.46410.14040.62140.0930.03520.48120.0210.651512.4963-92.7353-62.3817
52.08730.60380.59881.5403-0.03280.43250.12740.2224-0.52-0.672-0.27590.61160.01070.0571-0.04810.65850.1126-0.06930.4111-0.13550.65998.4387-94.2521-79.3077
63.891-2.0277-0.92363.43130.25632.8197-0.10660.16510.0430.1833-0.07320.66590.3945-0.85570.04020.2561-0.03660.05070.3183-0.0720.4491-0.064-71.149-64.7673
78.5718-2.72681.25674.62850.15833.28710.48660.31281.211-0.5846-0.297-0.6743-0.00570.0562-0.08660.32330.04680.040.21570.01470.349511.2863-70.6978-72.9476
85.00790.39811.80941.43710.53282.3589-0.2832-0.08641.3536-0.20940.2364-1.3952-0.0630.4603-0.12430.4366-0.0064-0.01210.4324-0.17910.908519.5103-82.4342-73.407
90.58590.8135-1.08493.690.43633.43920.16590.66950.4312-1.88590.01940.765-1.3287-0.10470.12650.82540.0892-0.22810.4773-0.10260.7365.9841-84.6983-84.832
100.84670.10820.40921.0167-0.94151.5333-0.3737-0.2406-0.4167-0.15050.5597-0.15530.3988-0.8521-0.09410.4055-0.04390.09640.52180.11630.42682.6989-79.4016-49.5127
110.30210.55870.02752.21050.76430.2378-0.3698-0.2731-0.27131.32720.5413-0.7772-0.2905-0.6279-0.08870.8391-0.01310.16730.90930.12570.90864.3298-89.0654-31.6612
121.77830.4436-0.93873.4469-1.21191.95280.0497-0.4807-0.86410.2895-0.1031-0.67630.55410.38940.05590.61970.0259-0.04780.71990.13850.574712.7528-81.7477-42.9709
132.290.4476-0.67913.5956-1.48823.10070.1403-0.74690.01860.7529-0.06150.0205-0.35710.0704-0.00940.36190.0043-0.01380.5606-0.00690.303212.4991-68.6162-46.0924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 154:184)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 185:203)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 204:218)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 219:247)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 248:262)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 263:280)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 281:301)
8X-RAY DIFFRACTION8CHAIN A AND (RESID 302:314)
9X-RAY DIFFRACTION9CHAIN A AND (RESID 315:335)
10X-RAY DIFFRACTION10CHAIN B AND (RESID 154:184)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 185:197)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 198:252)
13X-RAY DIFFRACTION13CHAIN B AND (RESID 253:335)

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