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- PDB-8efm: Structure of coral STING receptor from Stylophora pistillata in c... -

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Basic information

Entry
Database: PDB / ID: 8efm
TitleStructure of coral STING receptor from Stylophora pistillata in complex with 2',3'-cGAMP
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / immune receptor / cGAS-STING / coral / innate immunity
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
cGAMP / Stimulator of interferon genes protein 1
Similarity search - Component
Biological speciesStylophora pistillata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsLi, Y. / Slavik, K.M. / Morehouse, B.R. / Mears, K. / 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
DepositionSep 8, 2022Deposition 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
Revision 1.2Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)46,3125
Polymers45,4462
Non-polymers8673
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-27 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.765, 89.765, 174.778
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-401-

SO4

21A-578-

HOH

31B-582-

HOH

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Components

#1: Protein Stimulator of interferon genes protein


Mass: 22722.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stylophora pistillata (invertebrata) / Gene: Tmem173, AWC38_SpisGene6019 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2B4SJD2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% PEG 5000 MME, 100 mM Tris-HCl pH 8.6, 200 mM lithium sulfate

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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: Feb 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.13→38.87 Å / Num. obs: 23858 / % possible obs: 99.8 % / Redundancy: 13.6 % / CC1/2: 0.998 / Net I/σ(I): 14.6
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 8.9 % / Num. unique obs: 23858 / CC1/2: 0.484 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.13→38.87 Å / SU ML: 0.2069 / Cross valid method: FREE R-VALUE / Phase error: 20.0255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 2095 8.81 %
Rwork0.1974 21689 -
obs0.1999 23784 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.74 Å2
Refinement stepCycle: LAST / Resolution: 2.13→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 55 196 3105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023039
X-RAY DIFFRACTIONf_angle_d0.53174121
X-RAY DIFFRACTIONf_chiral_restr0.0409444
X-RAY DIFFRACTIONf_plane_restr0.0044506
X-RAY DIFFRACTIONf_dihedral_angle_d12.65231112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.180.28721200.25851239X-RAY DIFFRACTION87.79
2.18-2.240.28171360.21711409X-RAY DIFFRACTION98.91
2.24-2.30.23151370.21921420X-RAY DIFFRACTION99.68
2.3-2.360.28881390.21961438X-RAY DIFFRACTION100
2.36-2.440.25141360.20841412X-RAY DIFFRACTION99.94
2.44-2.530.23681380.20581430X-RAY DIFFRACTION100
2.53-2.630.22311400.20821445X-RAY DIFFRACTION100
2.63-2.750.23571380.20911424X-RAY DIFFRACTION99.94
2.75-2.890.25251410.21291467X-RAY DIFFRACTION100
2.89-3.070.22961390.20511441X-RAY DIFFRACTION100
3.07-3.310.24381410.19571466X-RAY DIFFRACTION100
3.31-3.640.21531430.18241467X-RAY DIFFRACTION100
3.64-4.170.20941430.16971482X-RAY DIFFRACTION100
4.17-5.250.17311460.15991517X-RAY DIFFRACTION100
5.25-38.870.22081580.21781632X-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)
12.892553969671.55007366511-0.7447309026542.05454298726-0.1258709783151.926082951020.1099549229660.450139163926-0.460792487606-0.350070755491-0.06890739224630.374036032940.5151690869730.332280646914-0.07929995398190.2295790377250.0315257429932-0.1086477269160.1308360337370.00202427789850.21027973623311.90062166620.279583625969.7606495724
23.580354593061.653084219861.605434447116.194090384681.042820471933.93177939371-0.05452321041130.404950086114-0.236888908925-0.07864535016340.125477109697-0.270084570841-0.0745656398740.714317478280.1087379980920.06802968968610.003131430942330.01507183593960.03781130330510.07218260354280.025571846715220.831917848934.07625730775.9234052784
32.609492297281.432955282480.415249757270.9146903201640.8265640688563.06353673542-0.175364871517-0.0955869594707-0.2218107124610.366815980098-0.0455496637099-0.503958951027-0.3277765875270.295814643688-0.1005830683370.291713880479-0.0062885034989-0.1137619084370.1871197116050.03024442915140.11795080866225.49695349336.477815851387.777157996
41.39315504115-2.326731966160.3141773308456.095177432462.850155431655.68060687083-0.214183024527-0.638596883704-0.8927529279620.768492662081-0.1205171629871.478089212981.09766279136-1.13255655039-1.580012489660.2036909786580.0439940622884-0.03653263762920.2509787334560.2199841068270.39604794403812.729569512117.611942144385.8147177788
50.978350844104-0.432853830847-0.009110523646521.06135809220.1426238234260.625250324036-0.114210285313-0.514662632165-0.6890529843930.2769019707230.426200416630.563000016822-0.193956785605-0.726421470807-0.3664973228050.1725947302790.03557802149760.05009926791810.3481772241470.2351340370070.26365746372514.051668471330.834230724890.6000378425
61.67347725296-0.3621425910311.002256628931.38725454109-0.5778281198763.41233450644-0.188179538046-0.0878581755154-0.03759517982630.2112578280150.05355908873790.0777415459357-0.242007758972-0.284524495934-0.121279131930.0953173098766-0.01113078109650.004100016224650.1806684699530.08183960237540.10803861765413.057194006933.10263829882.2485220786
70.640806976629-0.7434509411910.09257057925480.916478388488-0.03671045074961.488462443680.00705807793384-0.411429309095-0.3115771025160.489426535358-0.0428333294744-0.227973659319-0.0817282116422-0.39793637007-0.1711018107570.315911766553-0.00705161484593-0.06710641758130.1965183748680.1110785793170.13632227610923.782612775324.524478407495.7882343246
82.75797544513-0.8628996499321.432722022572.476014067963.387036367777.4160101623-0.130576405261-0.643347640781-0.6916987407410.527544825928-0.3004169631010.3734624119230.338735775357-1.11623634144-0.4458812592070.5339758012330.0947392132685-0.08360451205150.2277780424140.08543402116520.4497986462192.129515941214.265505476679.6699594458
91.42757613481.229194878290.4472531719393.23658241161-0.2848333728141.03155591387-0.1553808748380.369750277075-1.21182707172-0.3520194212770.09761119953440.4567149903210.524977369790.2941267470580.2571546574270.3108462460750.0668415722076-0.0628400101981-0.0146851447831-0.05874547300330.56639266580313.460093384811.04002768274.2252054206
104.24260303161-1.039853638561.372766943967.426175334934.104275785283.2068746152-0.1763870301381.174309079920.279740777303-1.272533523890.12204028461-0.571862214256-0.4174510306310.147924132291-0.2310605379220.262286293611-0.04418399806130.08259081151580.3185238862970.01757459176790.22709016957825.871395109825.743373319370.6754136165
115.189273135432.44345292823-2.295136871183.6773723887-1.640497190883.350167099020.282989162007-1.0635187778-0.9771252696360.530713337401-0.2817866385050.2443844290260.5229752201760.04645123345130.3088310200140.31334069318-0.0497067518747-0.0255300706770.3040869717350.1848283812430.41139628686718.297657416715.675384324187.0617597711
122.10925079729-0.557736953006-0.1181911565550.993943368576-0.1894984443161.144326030310.1456461797640.259769185513-0.226437102581-0.0927136789838-0.427419229898-0.2046542595030.2154445472760.469972715708-0.5359590244570.3171555452680.0303348435562-0.2145272391720.2480498978970.294458171210.23351869865126.570119805719.218663868491.0386295911
132.23956505933-0.651475254607-0.2869548317513.4283850263-0.08648258982722.462509545940.05107137623480.160890713403-0.167083512634-0.254570646281-0.1387067779630.269230534596-0.07459192305790.174212884880.05746224392170.07305520963550.01051646943950.002471345472670.1972326357510.02669333835180.124651744271-4.2373486245337.05847230171.0937807002
143.50069855028-1.76151845865-0.05153110535812.61441353350.596277817641.96795349708-0.253998310280.0981246185577-0.45720074479-0.08235588989180.002294699149970.5802840598170.253621020062-0.119718651777-0.1503674176790.178719601779-0.0187974116565-0.08694602566810.204036423232-0.06217616093710.310883582546-2.6668890080825.24387261763.1530060858
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 181 through 194 )AA181 - 1941 - 14
22chain 'A' and (resid 195 through 207 )AA195 - 20715 - 27
33chain 'A' and (resid 208 through 220 )AA208 - 22028 - 40
44chain 'A' and (resid 221 through 234 )AA221 - 23441 - 53
55chain 'A' and (resid 235 through 253 )AA235 - 25354 - 72
66chain 'A' and (resid 254 through 273 )AA254 - 27373 - 92
77chain 'A' and (resid 274 through 289 )AA274 - 28993 - 108
88chain 'A' and (resid 290 through 307 )AA290 - 307109 - 123
99chain 'A' and (resid 308 through 327 )AA308 - 327124 - 143
1010chain 'A' and (resid 328 through 335 )AA328 - 335144 - 151
1111chain 'A' and (resid 336 through 349 )AA336 - 349152 - 163
1212chain 'A' and (resid 350 through 361 )AA350 - 361164 - 175
1313chain 'B' and (resid 181 through 289 )BD181 - 2891 - 107
1414chain 'B' and (resid 290 through 359 )BD290 - 359108 - 172

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