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- PDB-8efn: Structure of Sp-STING3 from Stylophora pistillata coral in comple... -

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Basic information

Entry
Database: PDB / ID: 8efn
TitleStructure of Sp-STING3 from Stylophora pistillata coral in complex with 3',3'-cGAMP
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / immune receptor / cGAS-STING / coral / innate immunity
Function / homology
Function and homology information


3',3'-cyclic GMP-AMP binding / cyclic-di-AMP binding / 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 ...3',3'-cyclic GMP-AMP binding / cyclic-di-AMP binding / 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
Chem-4BW / Stimulator of interferon genes protein 3
Similarity search - Component
Biological speciesStylophora pistillata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stimulator of interferon genes protein
D: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6987
Polymers42,7752
Non-polymers9235
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-8 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.469, 82.702, 84.796
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Stimulator of interferon genes protein


Mass: 21387.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stylophora pistillata (invertebrata) / Gene: Tmem173, AWC38_SpisGene6026 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2B4SES9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-4BW / 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one / 3',3' cGAMP / c-GMP-AMP / c[G(3',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.: 223 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 19% PEG 3350, 100 mM Bis-Tris propane, pH 6.4, 250 mM MgCl2

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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: 1.73→38.84 Å / Num. obs: 38535 / % possible obs: 99.9 % / Redundancy: 12.3 % / CC1/2: 0.998 / Net I/σ(I): 12.4
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 3.6 % / Num. unique obs: 38535 / CC1/2: 0.678 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EFM

8efm


Resolution: 1.73→38.84 Å / SU ML: 0.1564 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.2416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1951 2005 5.21 %
Rwork0.1709 36469 -
obs0.1721 38474 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.87 Å2
Refinement stepCycle: LAST / Resolution: 1.73→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 61 223 3136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353026
X-RAY DIFFRACTIONf_angle_d0.72844096
X-RAY DIFFRACTIONf_chiral_restr0.0501444
X-RAY DIFFRACTIONf_plane_restr0.005500
X-RAY DIFFRACTIONf_dihedral_angle_d13.83361116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.29491440.27272546X-RAY DIFFRACTION98.53
1.77-1.820.24191310.22722553X-RAY DIFFRACTION99.85
1.82-1.870.23541430.1992577X-RAY DIFFRACTION99.93
1.87-1.940.20631460.17212557X-RAY DIFFRACTION100
1.94-20.211350.18062578X-RAY DIFFRACTION100
2-2.080.19761480.17382580X-RAY DIFFRACTION100
2.08-2.180.20941390.16522583X-RAY DIFFRACTION100
2.18-2.290.18621440.15812574X-RAY DIFFRACTION100
2.29-2.440.18561430.16592613X-RAY DIFFRACTION100
2.44-2.630.19021460.17142604X-RAY DIFFRACTION100
2.63-2.890.20811450.16982610X-RAY DIFFRACTION100
2.89-3.310.21021450.16882641X-RAY DIFFRACTION100
3.31-4.170.1781430.15122664X-RAY DIFFRACTION100
4.17-38.840.16411530.16542789X-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)
12.491534228021.40697833522-0.9025232680583.22609166737-0.3280594990341.55232763544-0.0678412104972-0.10596679967-0.1965200963640.259475325674-0.0713424964014-0.02977241904920.117466745507-0.07777484717110.1002915523160.1107675470840.001738262894560.02152117748420.09225176724730.003193258943560.097666379603515.756399362956.994005874234.0912888372
20.4399179203810.3361243984420.003099629695822.949732204031.324193895480.6261884590990.02003706403440.06256148428820.01881162636090.014375953248-0.1765330551110.30040904874-0.0175567186452-0.1185716673320.1809970788290.1125326219320.004684883424240.01571998344930.1485248656430.006747061208680.1368479666649.5614098458559.058657836226.0243529061
31.048443203020.184015315764-0.05576566854481.544238563070.6023131364391.47461690815-0.0573620460510.0925872879268-0.155532220379-0.36191069561-0.2233116866590.149007104929-0.0357847274419-0.1070485022920.1060261759030.1636500333950.01983083927650.009294930115360.106522390432-0.03814712895740.1673920025811.202046053157.856991684521.7944883089
42.143344570151.29832323738-0.7340189886653.344916323850.306438788441.66050685349-0.05309007830170.0709597864621-0.216149013768-0.04559307990250.043902824688-0.20397380812-0.0591011142482-0.01271461435490.01024981233810.1026784287090.04951843304810.02306843034530.114182446688-0.008641604582860.16437124491421.092895771251.995937235221.6706083102
52.63253853073-1.47054699708-0.7597915551693.062180969370.9947883204911.972608278790.0514499266418-0.07562954790990.11416340509-0.205136507111-0.03162826966190.189630464613-0.113962800732-0.2909889948040.01590427997150.08231899330120.0119538581216-0.02197916121620.1578865241440.0107610481250.09755736371959.8775318337780.863344582225.3038601205
60.7505918273570.107317459007-0.01929034368552.40272693491.062907826761.093429147980.0402979609978-0.09860500745190.008565545155930.248089983077-0.1113597853140.160625212170.0479362138396-0.04957784281730.07887290028270.09807635631140.01555882919220.005380978354850.1070405831310.01518153685860.073897210702513.893741896778.781837825334.2359534674
72.29131561979-0.544710280854-0.1027174521752.034476096330.03346364143231.778211636090.126895956895-0.03733231220480.1194764158580.130034612314-0.079443211259-0.275921470294-0.01833090150970.0597819865187-0.0686461675210.107051629281-0.0399465835895-0.0236928629530.08092628772890.009128819922410.11802257786422.958967049279.743422926734.1077991255
81.65578745647-0.0867666067946-0.3722850957852.384892256590.9672598822021.88895877399-0.003997403842770.0220283936680.0887597865624-0.2010215179470.0941716748823-0.122462709715-0.1710401358730.0583049164712-0.08305151887250.145274861359-0.03418252676270.01997659787480.1111471771990.04657490371630.097411842649823.429955726185.64844663625.2317699086
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 170 through 209 )AA170 - 2091 - 40
22chain 'A' and (resid 210 through 249 )AA210 - 24941 - 80
33chain 'A' and (resid 250 through 292 )AA250 - 29281 - 123
44chain 'A' and (resid 293 through 344 )AA293 - 344124 - 175
55chain 'D' and (resid 170 through 209 )DD170 - 2091 - 40
66chain 'D' and (resid 210 through 260 )DD210 - 26041 - 91
77chain 'D' and (resid 261 through 292 )DD261 - 29292 - 123
88chain 'D' and (resid 293 through 344 )DD293 - 344124 - 175

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