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- PDB-8gjz: Structure of a STING receptor from S. pistillata Sp-STING1 bound ... -

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Basic information

Entry
Database: PDB / ID: 8gjz
TitleStructure of a STING receptor from S. pistillata Sp-STING1 bound to 2'3'-cUA
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / STING / cyclic dinucleotide / innate immunity / cGAS
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / reticulophagy / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / autophagosome / innate immune response / endoplasmic reticulum membrane
Similarity search - Function
Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain
Similarity search - Domain/homology
2'3'-cUA / Stimulator of interferon genes protein 1
Similarity search - Component
Biological speciesStylophora pistillata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsLi, Y. / Toyoda, H. / Slavik, K.M. / Morehouse, B.R. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: Cell / Year: 2023
Title: cGLRs are a diverse family of pattern recognition receptors in innate immunity.
Authors: Li, Y. / Slavik, K.M. / Toyoda, H.C. / Morehouse, B.R. / de Oliveira Mann, C.C. / Elek, A. / Levy, S. / Wang, Z. / Mears, K.S. / Liu, J. / Kashin, D. / Guo, X. / Mass, T. / Sebe-Pedros, A. / ...Authors: Li, Y. / Slavik, K.M. / Toyoda, H.C. / Morehouse, B.R. / de Oliveira Mann, C.C. / Elek, A. / Levy, S. / Wang, Z. / Mears, K.S. / Liu, J. / Kashin, D. / Guo, X. / Mass, T. / Sebe-Pedros, A. / Schwede, F. / Kranzusch, P.J.
History
DepositionMar 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)44,3453
Polymers43,7102
Non-polymers6351
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-12 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.429, 113.429, 259.272
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Stimulator of interferon genes protein


Mass: 21854.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal Serine residue is from tag, not part of the biological protein sequence.
Source: (gene. exp.) Stylophora pistillata (invertebrata) / Gene: Tmem173 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2B4SJD2
#2: Chemical ChemComp-ZNT / 2'3'-cUA / 1-[(2R,5R,7R,8R,10S,12aR,14R,15R,15aS,16R)-14-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxooctahydro-2H,10H,12H-5,8-methano-2lambda~5~,10lambda~5~-furo[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-7-yl]pyrimidine-2,4(1H,3H)-dione


Mass: 635.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 5.51 Å3/Da / Density % sol: 77.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.4 M NaCl, 100 mM HEPES, pH 7.2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.92→49.12 Å / Num. obs: 22222 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 68.92 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.7
Reflection shellResolution: 2.92→3.1 Å / Num. unique obs: 3490 / CC1/2: 0.607

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→49.12 Å / SU ML: 0.3828 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2167 2000 9.03 %
Rwork0.1957 20142 -
obs0.1977 22142 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.66 Å2
Refinement stepCycle: LAST / Resolution: 2.92→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 42 6 3021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00183135
X-RAY DIFFRACTIONf_angle_d0.48054249
X-RAY DIFFRACTIONf_chiral_restr0.0391459
X-RAY DIFFRACTIONf_plane_restr0.0036529
X-RAY DIFFRACTIONf_dihedral_angle_d10.74181153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-2.990.42631390.35291392X-RAY DIFFRACTION99.03
2.99-3.080.33121390.3211410X-RAY DIFFRACTION99.87
3.08-3.170.28661390.28631403X-RAY DIFFRACTION100
3.17-3.270.29391400.25261401X-RAY DIFFRACTION99.94
3.27-3.390.30431410.24351415X-RAY DIFFRACTION99.81
3.39-3.520.2991370.22341391X-RAY DIFFRACTION99.03
3.52-3.680.20931410.20721424X-RAY DIFFRACTION99.94
3.68-3.870.19441420.18321429X-RAY DIFFRACTION100
3.87-4.120.20221430.16341428X-RAY DIFFRACTION99.81
4.12-4.440.18621420.16471431X-RAY DIFFRACTION99.94
4.44-4.880.18271440.14641459X-RAY DIFFRACTION100
4.88-5.590.16011450.16771458X-RAY DIFFRACTION99.38
5.59-7.030.21711500.20451502X-RAY DIFFRACTION99.94
7.04-49.120.1881580.17751599X-RAY DIFFRACTION99.15
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)
16.927591396720.7204452000085.02174206612.52570600786-0.4278406869145.86577241016-0.0321486676369-1.3289286280.6416121251780.2450036029440.3611214312740.272005004862-0.356674169669-0.1629051628910.2409058136660.377827744460.0138020583866-0.02578443537241.21678356083-0.4052114926810.920689649882-28.875935059654.52752123186.23390988437
25.841094917231.396119491645.82192567715.93329666371.340681156985.94632926595-0.763481409380.6585796092971.45789342983-0.7431595902610.007679017694850.269378953161-0.8552338841460.9235428326370.3492741488710.471179824829-0.1479458001580.02024907348170.804285322799-0.0820019662880.703476339058-34.734243758557.2489393268-11.8969215214
34.633880312771.360371077030.3038300752823.62258702639-1.019306075727.15598761655-0.113959613595-0.714440036624-0.302148012938-0.2370072264-0.0377603849835-0.05670721168890.252053037657-0.1544661336440.1608699161340.2721222224140.0073192230370.028870523430.52078644196-0.06978444179530.552120660355-41.183275652445.0568418837-10.3493508038
43.168868286812.08320143468-0.879385150554.42509152988-0.2387291945093.4243787413-0.288153807445-0.85060661729-0.253648292631-0.1043878031860.0319249874744-0.426229760567-0.1629899226120.2821561560810.3242425175520.427318044187-0.01477381109280.1201654911980.812376141618-0.1283063340190.799227945144-39.147444998646.8720379405-12.2805356694
56.98827193121-0.2033072514632.444344474732.43583278306-0.5556478865817.23192080716-0.0804720516008-1.46045663947-0.4486017333790.3366988662130.198753234478-0.3649407454320.08791182205130.0329285463287-0.09338199652010.3497371952150.01029190588370.05294422536461.01661866286-0.08682959704430.815261298339-37.389206046147.10228600564.09615785094
65.76563406031.01487143285-0.9874231209185.85595479873-0.9279601347465.15472607237-0.4876964909870.653228367027-0.1822870868040.06932129759560.3312482854220.662192583289-0.301450451618-0.6371085259580.1274776064980.375063471806-0.05326962564830.1175523003391.08202178597-0.1713196250220.57783505306-52.193277405446.2179660254-4.0357252285
77.662019761651.84722629687-1.046346748323.805717901181.614670893755.75893983563-0.1451649114630.691209067144-0.668183787375-0.2088708032570.0637909598576-0.01733046849460.2768111028380.1109417680580.01952923661640.3380877748480.0535107735813-0.02840728283450.790644889285-0.167630614960.783536001181-12.98536513244.403024438-4.31125059601
88.099601521171.835139476322.425526952161.40815051836-0.3758028047471.58592706534-0.3935872066031.62209678223-0.186733401499-0.1593849336150.2271349417850.0160966864252-0.1631481028720.1918378594820.198631433070.516089819237-0.00812401288966-0.005267779464081.24192588688-0.1713604890810.830744229315-8.9906270781948.3346884256-12.6210377776
98.56746185661-0.0521551225765-0.6244554966055.739474665361.170858456056.4428118281-0.179633085991-0.5386501201660.5879564776370.30837131132-0.02782933180780.268937287008-0.222303865193-0.2897518707360.1803336084860.265867436010.0675140149875-0.0102558949980.880716384056-0.1307207745210.674067795352-17.108565670752.74150590997.66409581503
107.158053478562.54445152495-1.439045639332.75009683017-1.084604368156.56648865272-0.2694514488961.02841605353-0.0919422068269-0.2339883576160.3291161478910.179823747363-0.4641757971730.575567293874-0.05728996449460.3611629617180.02971421957-0.1381728837761.15282213708-0.08365016544490.69450627183-1.2705570540551.7030019453-1.78267072982
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 180 through 193 )AA180 - 1931 - 14
22chain 'A' and (resid 194 through 208 )AA194 - 20815 - 29
33chain 'A' and (resid 209 through 253 )AA209 - 25330 - 74
44chain 'A' and (resid 254 through 278 )AA254 - 27875 - 99
55chain 'A' and (resid 279 through 346 )AA279 - 346100 - 167
66chain 'A' and (resid 347 through 360 )AA347 - 360168 - 181
77chain 'B' and (resid 180 through 235 )BB180 - 2351 - 56
88chain 'B' and (resid 236 through 289 )BB236 - 28957 - 110
99chain 'B' and (resid 290 through 335 )BB290 - 335111 - 156
1010chain 'B' and (resid 336 through 361 )BB336 - 361157 - 182

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