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- PDB-6a04: Structure of pSTING complex -

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Basic information

Entry
Database: PDB / ID: 6a04
TitleStructure of pSTING complex
ComponentsStimulator of interferon genes protein
KeywordsSIGNALING PROTEIN / pSTING
Function / homology
Function and homology information


proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / cGAS/STING signaling pathway / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / autophagosome ...proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / cGAS/STING signaling pathway / reticulophagy / autophagosome membrane / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / autophagosome / signaling adaptor activity / activation of innate immune response / positive regulation of interferon-beta production / endoplasmic reticulum-Golgi intermediate compartment membrane / cytoplasmic vesicle / defense response to virus / mitochondrial outer membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / perinuclear region of cytoplasm / protein homodimerization activity / plasma membrane / cytoplasm
Similarity search - Function
Stimulator of interferon genes protein / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsYuan, Z.L. / Shang, G.J. / Cong, X.Y. / Gu, L.C.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Crystal structures of porcine STINGCBD-CDN complexes reveal the mechanism of ligand recognition and discrimination of STING proteins.
Authors: Cong, X. / Yuan, Z. / Du, Y. / Wu, B. / Lu, D. / Wu, X. / Zhang, Y. / Li, F. / Wei, B. / Li, J. / Wu, J. / Xu, S. / Wang, J. / Qi, J. / Shang, G. / Gu, L.
History
DepositionJun 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8388
Polymers45,6682
Non-polymers1,1716
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-67 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.692, 63.950, 101.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Stimulator of interferon genes protein / / poSTING / Transmembrane protein 173


Mass: 22833.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TMEM173, STING / Production host: Escherichia coli (E. coli) / References: UniProt: B8XX90
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.77 Å3/Da / Density % sol: 30.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.5 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25599 / % possible obs: 97.9 % / Redundancy: 6.6 % / Net I/σ(I): 42.2
Reflection shellResolution: 1.9→1.97 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.9→31.053 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2496 1301 5.08 %
Rwork0.2021 --
obs0.2044 25599 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→31.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 71 119 3129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073083
X-RAY DIFFRACTIONf_angle_d0.8884195
X-RAY DIFFRACTIONf_dihedral_angle_d17.661875
X-RAY DIFFRACTIONf_chiral_restr0.054448
X-RAY DIFFRACTIONf_plane_restr0.005551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8999-1.9760.28051270.22092691X-RAY DIFFRACTION98
1.976-2.06590.29021490.22182714X-RAY DIFFRACTION100
2.0659-2.17480.28531530.20292712X-RAY DIFFRACTION100
2.1748-2.3110.2641290.20562734X-RAY DIFFRACTION100
2.311-2.48940.22111410.21172740X-RAY DIFFRACTION100
2.4894-2.73970.27841640.22642727X-RAY DIFFRACTION100
2.7397-3.13580.27331550.22622754X-RAY DIFFRACTION100
3.1358-3.94960.23131660.18772600X-RAY DIFFRACTION94
3.9496-31.05670.22481170.18352626X-RAY DIFFRACTION89
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)
18.1879-0.6622-0.06718.0984-2.55624.87250.06010.3456-0.4443-0.2752-0.1852-0.20230.31690.46730.09660.24670.00470.01710.29590.01570.193515.17420.097-16.2579
29.67790.1496-6.79964.7392-1.16928.09120.50030.48260.70980.0429-0.07830.2441-0.484-0.6206-0.48710.27580.04270.01390.25580.04840.2632-6.4419.0301-6.9652
37.3925-1.6311-0.88210.25080.31953.747-0.0821-0.0433-0.21090.06060.2160.1660.1424-0.1978-0.09960.293-0.0003-0.00340.28060.04540.2644-1.3623-1.0867-1.296
40.45120.1886-0.1070.1521-0.27473.58120.09130.0297-0.1158-0.0583-0.02090.02950.2007-0.2011-0.09330.2157-0.02040.01070.30230.01060.2895-6.0704-1.0484-10.6831
52.9146-1.2377-1.32413.30921.46282.2297-0.0125-0.0628-0.153-0.1393-0.00260.0016-0.04380.01310.0950.2364-0.0408-0.0450.24990.05220.25793.704-8.2462-5.4059
63.8424-1.32790.11092.535-0.76392.63030.0015-0.10030.06530.14580.0146-0.5716-0.09290.3593-0.01730.2497-0.0068-0.01990.31430.00430.225617.509-2.3547-7.7381
75.7312.1686-1.27919.6405-1.88646.68090.08270.07631.20450.65670.0944-0.0491-1.31870.3363-0.20070.3618-0.08970.00640.28540.02410.35287.34387.0089-2.0021
86.2438-2.8407-3.23345.87051.7856.8598-0.26920.0265-1.44160.0477-0.332-0.46831.87310.14550.48320.57770.0761-0.01250.40840.11340.55510.3403-14.7915.4528
92.7497-0.553-1.02162.8104-2.1692.6712-0.0534-0.473-0.07860.3210.071-0.08580.07660.0479-0.06050.1849-0.042-0.02710.21290.0020.30853.217-0.2758.601
105.50061.3423-0.54872.77070.06182.59840.09730.1172-0.1810.17670.0734-0.59920.17920.4962-0.18350.44770.0689-0.05860.37240.05720.333115.8804-2.081-21.6612
113.29511.56983.97214.7773-0.4818.29530.1171-0.0711-0.78430.2073-0.11780.08590.9932-0.2855-0.00410.4182-0.06950.11130.2683-0.04860.2938-4.8773-10.37-31.4397
123.5760.32180.61880.85060.17112.99090.04540.1528-0.1068-0.0635-0.0667-0.00670.0834-0.16510.03830.28140.03870.02930.2760.01660.1993-2.06732.5058-36.5644
134.53790.38140.96484.63271.22780.87010.0757-0.181-0.16240.1859-0.04960.3190.1658-0.3126-0.03470.2233-0.00190.04490.2441-0.00220.2115-5.6331.5286-35.1888
145.41660.09150.67723.97131.86844.4029-0.05940.24860.23820.14370.3329-0.437-0.04470.5176-0.30680.23390.01580.01790.36960.02790.270716.73026.175-26.2554
155.2311.85410.08510.73790.6355.7970.0146-0.1218-0.4442-0.13470.3062-0.2020.258-0.38-0.24640.16680.0053-0.01660.36130.01740.26848.5709-0.1214-37.7184
167.00060.8296-0.21875.20325.09175.12910.00230.8875-0.3549-0.64210.3644-0.5163-0.2969-0.0551-0.39860.2614-0.0250.0020.4270.03940.27124.0195-1.5505-46.9919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 151 through 166 )
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 211 )
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 242 )
5X-RAY DIFFRACTION5chain 'A' and (resid 243 through 280 )
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 301 )
7X-RAY DIFFRACTION7chain 'A' and (resid 302 through 314 )
8X-RAY DIFFRACTION8chain 'A' and (resid 315 through 324 )
9X-RAY DIFFRACTION9chain 'A' and (resid 325 through 337 )
10X-RAY DIFFRACTION10chain 'B' and (resid 151 through 165 )
11X-RAY DIFFRACTION11chain 'B' and (resid 166 through 185 )
12X-RAY DIFFRACTION12chain 'B' and (resid 186 through 218 )
13X-RAY DIFFRACTION13chain 'B' and (resid 219 through 262 )
14X-RAY DIFFRACTION14chain 'B' and (resid 263 through 299 )
15X-RAY DIFFRACTION15chain 'B' and (resid 300 through 324 )
16X-RAY DIFFRACTION16chain 'B' and (resid 325 through 340 )

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