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- PDB-6wt6: Structure of a metazoan TIR-STING receptor from C. gigas -

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Basic information

Entry
Database: PDB / ID: 6wt6
TitleStructure of a metazoan TIR-STING receptor from C. gigas
ComponentsMetazoan TIR-STING fusion
KeywordsIMMUNE SYSTEM / TIR domain / cyclic dinucleotide receptor / immune effector
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP binding / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / cyclic-di-GMP binding / NAD+ nucleotidase, cyclic ADP-ribose generating / reticulophagy / positive regulation of macroautophagy / autophagosome assembly / positive regulation of type I interferon production / activation of innate immune response / autophagosome ...2',3'-cyclic GMP-AMP binding / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / cyclic-di-GMP binding / NAD+ nucleotidase, cyclic ADP-ribose generating / 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 / signal transduction
Similarity search - Function
: / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily
Similarity search - Domain/homology
Stimulator of interferon genes protein
Similarity search - Component
Biological speciesCrassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å
AuthorsMorehouse, B.R. / Govande, A.A. / Millman, A. / Keszei, A.F.A. / Lowey, B. / Ofir, G. / Shao, S. / Sorek, R. / Kranzusch, P.J.
CitationJournal: Nature / Year: 2020
Title: STING cyclic dinucleotide sensing originated in bacteria.
Authors: Morehouse, B.R. / Govande, A.A. / Millman, A. / Keszei, A.F.A. / Lowey, B. / Ofir, G. / Shao, S. / Sorek, R. / Kranzusch, P.J.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metazoan TIR-STING fusion


Theoretical massNumber of molelcules
Total (without water)47,0631
Polymers47,0631
Non-polymers00
Water1,09961
1
A: Metazoan TIR-STING fusion

A: Metazoan TIR-STING fusion


Theoretical massNumber of molelcules
Total (without water)94,1272
Polymers94,1272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5130 Å2
ΔGint-28 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.424, 136.424, 40.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

#1: Protein Metazoan TIR-STING fusion


Mass: 47063.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crassostrea gigas (Pacific oyster) / Gene: XP_011430837.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DUE1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5, and 16% PEG-4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→48.05 Å / Num. obs: 15377 / % possible obs: 99.9 % / Redundancy: 16 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.094 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 1562 / CC1/2: 0.797 / Rpim(I) all: 0.691

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.41→48.05 Å / SU ML: 0.2777 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8814
RfactorNum. reflection% reflection
Rfree0.2416 1530 9.99 %
Rwork0.2156 --
obs0.2183 15312 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.31 Å2
Refinement stepCycle: LAST / Resolution: 2.41→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 0 61 2531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312523
X-RAY DIFFRACTIONf_angle_d0.56783412
X-RAY DIFFRACTIONf_chiral_restr0.0417379
X-RAY DIFFRACTIONf_plane_restr0.0042439
X-RAY DIFFRACTIONf_dihedral_angle_d11.41041529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.480.29911320.27781196X-RAY DIFFRACTION98.22
2.48-2.570.28661340.26531219X-RAY DIFFRACTION99.63
2.57-2.680.29351390.26291246X-RAY DIFFRACTION99.64
2.68-2.80.2971340.25171206X-RAY DIFFRACTION99.63
2.8-2.940.26981370.2461237X-RAY DIFFRACTION99.71
2.94-3.130.26611390.2371249X-RAY DIFFRACTION100
3.13-3.370.271390.23271240X-RAY DIFFRACTION99.78
3.37-3.710.22551380.19341256X-RAY DIFFRACTION99.93
3.71-4.250.21621390.18881256X-RAY DIFFRACTION99.93
4.25-5.350.20121440.17181295X-RAY DIFFRACTION100
5.35-48.050.22481550.22031382X-RAY DIFFRACTION99.93
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)
10.499882114972-0.03888487171490.02270236405811.075909092480.8521493769830.6834709308150.04490696608390.7386234120620.0176379839596-0.2780106636820.383082939202-0.206834388262-0.04185551181340.803710499110.07110487908160.313284930527-0.0132519026087-0.0282201843120.9428195213140.08587162338020.58767859521473.281132983136.9697149897-6.31289864246
20.5038902818990.405597146922-0.0972935554930.403112537221-0.5155464668563.37927097464-0.2139280789881.12058841365-0.210421354243-0.271973486735-0.0768704185405-0.3788060508120.3818520309310.7603012002670.04704163605110.339263250223-0.0951615355765-0.04389366077470.8246320465680.2435789600590.64289258890163.677475047340.5937476073-11.4591530285
33.03879386135-2.10208657968-0.5995327229561.571252748980.7817572484651.25178722471-0.2869185234350.3028616644591.63618120029-0.2589524514780.2514542601-1.05443589749-1.359593354420.5763752273580.2149622023260.604443808595-0.148581860903-0.1239638700640.5881099007670.05389725079990.72015665387264.592407545451.0754969361-3.18608266847
41.59890473414-0.0266373694321-0.3562281774230.7474457960460.1867850367191.963387102070.0115687455323-0.0825015100480.02386545643060.123967628766-0.03412210830660.0403975693808-0.00593151403894-0.333615030722-0.04626382695490.1214947323390.00604223946532-0.001666822122720.178311894801-0.00182651440620.13708725243628.616970284245.92283739547.06039298712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 150 )
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 358 )

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