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- PDB-8gjy: Structure of a cGAS-like receptor Sp-cGLR1 from S. pistillata -

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Basic information

Entry
Database: PDB / ID: 8gjy
TitleStructure of a cGAS-like receptor Sp-cGLR1 from S. pistillata
ComponentscGAS-like receptor 1
KeywordsIMMUNE SYSTEM / pattern recognition receptor / cGAS / innate immunity / cGAS-like receptor
Function / homologyMab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Protein mab-21-like 2
Function and homology information
Biological speciesStylophora pistillata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cGAS-like receptor 1


Theoretical massNumber of molelcules
Total (without water)44,1581
Polymers44,1581
Non-polymers00
Water7,584421
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.160, 41.319, 58.649
Angle α, β, γ (deg.)90.000, 91.800, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein cGAS-like receptor 1


Mass: 44157.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stylophora pistillata (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2B4RP11
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 275 mM Ammonium nitrate, 16% (w/v) PEG3350

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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 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→48.52 Å / Num. obs: 63374 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 15.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.4 % / Num. unique obs: 6220 / CC1/2: 0.949 / % possible all: 98.3

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Processing

Software
NameVersionClassification
AutoSolphasing
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→48.52 Å / SU ML: 0.1263 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.8474
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1801 1986 3.13 %
Rwork0.1706 61377 -
obs0.1709 63363 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.96 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 0 421 3274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562951
X-RAY DIFFRACTIONf_angle_d0.81563977
X-RAY DIFFRACTIONf_chiral_restr0.0489429
X-RAY DIFFRACTIONf_plane_restr0.0097506
X-RAY DIFFRACTIONf_dihedral_angle_d12.39721157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.21341360.18524298X-RAY DIFFRACTION98.64
1.54-1.580.20831430.18124342X-RAY DIFFRACTION99.4
1.58-1.630.19461410.19524355X-RAY DIFFRACTION99.62
1.63-1.680.21251420.18794338X-RAY DIFFRACTION99.6
1.68-1.740.2161340.18024382X-RAY DIFFRACTION99.3
1.74-1.810.20611500.1784324X-RAY DIFFRACTION98.68
1.81-1.890.21361390.17344381X-RAY DIFFRACTION99.69
1.89-1.990.22471400.18834364X-RAY DIFFRACTION99.58
1.99-2.110.19391430.16114372X-RAY DIFFRACTION99.73
2.11-2.280.17251480.1564383X-RAY DIFFRACTION99.67
2.28-2.510.17921420.16814393X-RAY DIFFRACTION99.36
2.51-2.870.17841390.16944432X-RAY DIFFRACTION99.78
2.87-3.620.1741430.16784449X-RAY DIFFRACTION99.89
3.62-48.520.15231460.16884564X-RAY DIFFRACTION99.7
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)
11.021058615450.9093266900311.2961284420.9607511148281.635765721795.61004600562-0.159848090790.1620957855160.127106403744-0.1339583147220.02409992352080.0615220973515-0.4921081215730.07462093461010.1684242332560.1336077866220.038918386123-0.02121318783580.09028445097230.00280640876130.12179568049267.389993380143.12589836648.131989724
21.790458879180.05806039176360.2283031193260.97284423251-0.09039453614861.77559664749-0.09241489835850.233902474620.0106613957544-0.02064665478090.08857590383510.08777467153710.00152257811048-0.01128326005160.005272216945340.142276298448-0.0005514546934840.01411049307170.179984319376-0.009349132174760.11740481179756.391559978129.3621206340.019530415
30.9819056424570.217458887894-0.7552498699790.416428552537-0.07450218800022.18905117648-0.105577405090.125936389678-0.0849933230243-0.08993623572870.03755456290190.0005915973959090.160830257072-0.02401080345590.05902542430560.1164105869840.000515479367157-0.008300121180850.147500879196-0.01004112125420.12393216991255.451324578927.181725415839.1312704089
41.505819890810.538639696920.4984100798160.6076897642050.1844480303381.18954644260.0038344431498-0.07787379688750.00366923902930.0215078175332-0.02634332116960.0126756589199-0.0153034505081-0.03001244321630.01194840036550.1026639688980.0150628100571-0.006729616525480.086544506198-0.00381261687320.10806623614662.879577128331.614455471362.694150074
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 51 )8 - 511 - 44
22chain 'A' and (resid 52 through 113 )52 - 11345 - 95
33chain 'A' and (resid 114 through 244 )114 - 24496 - 219
44chain 'A' and (resid 245 through 376 )245 - 376220 - 344

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