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- PDB-7lt2: Structure of a dsRNA-sensing cGAS-like receptor from the beetle T... -

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Basic information

Entry
Database: PDB / ID: 7lt2
TitleStructure of a dsRNA-sensing cGAS-like receptor from the beetle Tribolium castaneum
ComponentsMab-21 domain-containing protein
KeywordsIMMUNE SYSTEM / cGAS-like receptor / cGLR / nucleotidyltransferase
Function / homology
Function and homology information


3',2'-cyclic GMP-AMP synthase activity / immune response involved in response to exogenous dsRNA / cyclic GMP-AMP synthase / double-stranded RNA binding / defense response to virus / innate immune response / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Beta Polymerase; domain 2 - #90 / Mab-21-like, nucleotidyltransferase domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Cyclic GMP-AMP synthase-like receptor
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsSlavik, K.M. / Morehouse, B.R. / Kranzusch, P.J.
CitationJournal: Nature / Year: 2021
Title: cGAS-like receptors sense RNA and control 3'2'-cGAMP signalling in Drosophila.
Authors: Slavik, K.M. / Morehouse, B.R. / Ragucci, A.E. / Zhou, W. / Ai, X. / Chen, Y. / Li, L. / Wei, Z. / Bahre, H. / Konig, M. / Seifert, R. / Lee, A.S.Y. / Cai, H. / Imler, J.L. / Kranzusch, P.J.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 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: Mab-21 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3892
Polymers46,3341
Non-polymers551
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-4 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.405, 70.443, 104.604
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 Mab-21 domain-containing protein / Tc-cGLR


Mass: 46334.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: TcasGA2_TC003965 / Production host: Escherichia coli (E. coli) / References: UniProt: D6WI29
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.3 M potassium thiocyanate, 10-16% 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: Oct 17, 2019
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.58→41.99 Å / Num. obs: 57602 / % possible obs: 98.4 % / Redundancy: 2.7 % / Biso Wilson estimate: 21.52 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.037 / Net I/σ(I): 9.6
Reflection shellResolution: 1.58→1.61 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2838 / CC1/2: 0.525 / Rpim(I) all: 0.612

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→41.99 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.1255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 2000 3.48 %
Rwork0.1858 55471 -
obs0.1868 57471 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.21 Å2
Refinement stepCycle: LAST / Resolution: 1.58→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 1 543 3731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373273
X-RAY DIFFRACTIONf_angle_d0.66044435
X-RAY DIFFRACTIONf_chiral_restr0.0444474
X-RAY DIFFRACTIONf_plane_restr0.0047568
X-RAY DIFFRACTIONf_dihedral_angle_d12.71881229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.39231410.34883906X-RAY DIFFRACTION97.82
1.62-1.660.35811400.30853893X-RAY DIFFRACTION97.75
1.66-1.710.33091430.27933973X-RAY DIFFRACTION98.75
1.71-1.770.25171440.23543963X-RAY DIFFRACTION99.11
1.77-1.830.24181430.21323991X-RAY DIFFRACTION99.45
1.83-1.90.24091440.21263970X-RAY DIFFRACTION98.54
1.9-1.990.28571390.25113879X-RAY DIFFRACTION96.91
1.99-2.10.23451440.18463983X-RAY DIFFRACTION98.92
2.1-2.230.21081440.17913997X-RAY DIFFRACTION99.07
2.23-2.40.22291440.19463996X-RAY DIFFRACTION98.15
2.4-2.640.18091400.17563891X-RAY DIFFRACTION96.16
2.64-3.020.1811480.17224070X-RAY DIFFRACTION99.41
3.02-3.810.1951410.1613954X-RAY DIFFRACTION95.66
3.81-41.990.19471450.15824005X-RAY DIFFRACTION93.05
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)
10.6248325661290.255379599850.04134754525110.478246488241-0.004060527359290.6006765617770.074579584638-0.0174377194167-0.05742333850620.281318008147-0.0293193119336-0.003998620030460.01566918345750.02900259198583.45635833508E-60.1946373748840.0206566048513-0.01045067642770.173803718646-0.004132821826710.16921096584127.804657341649.332477332243.4956840881
20.999786027162-0.226373903143-0.05912743845391.24108535561-0.4046124223391.045244778720.01089683884970.1766195160740.0563148467236-0.05704073983810.002284108739410.1679506575540.00268220728182-0.065740929729-6.29866857679E-50.1666922365950.012405165783-0.006473055841870.1862484571580.02059535829190.16252771481420.442651453169.062431457228.6542351335
30.9039085827950.03183292263840.09642550260321.15075736452-0.4616158806320.597131325470.02999111581720.255020642852-0.0133533963711-0.249848454692-0.170605194901-0.129363499924-0.1506466553360.314246775999-0.006797438703750.190512253990.03730334837040.01083526941890.211685046630.01786221744490.20187661840841.38785974652.454831269435.945663086
41.13994521002-0.1401302174810.07863580759890.589408637526-0.596707902394-0.0914332964554-0.008587721018170.210748658187-0.081307000357-0.1571603288430.06879086674830.1013589729220.0632525423502-0.01250225450930.04004507878120.2248469082680.011883684034-0.02794367617270.203218831033-0.002133146025540.18104351423214.118589465358.497734750733.3870478265
50.8287941888310.0219850785504-0.207493398830.8662831065080.7732267606921.022227354720.04724015463760.108415283959-0.07314184190970.149888049227-0.05831009223430.04467773563790.0518771167671-0.0952752156927-0.00686290471920.1643301497140.002815553764970.01343150396110.184160587127-0.005021029555860.1898128202339.9450601172438.33614609941.2487588574
61.179196179010.5493097849670.01722002660740.4187522210120.5322999675831.0416040271-0.01216981926570.255990926811-0.173895280874-0.17612018396-0.06021546123650.192361506513-0.0142167844086-0.142639413872-0.009911925277120.1884484537340.0271622249354-0.0265494447180.288279629455-0.04486542169040.2159350113116.5717657650435.417516549829.4178420231
70.308610298768-0.336771372322-0.07386306980910.949062015664-0.1193121290450.7294368106520.1353060381940.0386538514659-0.3928877599880.161398349765-0.0745555156183-0.1522894585010.225604194665-0.03506086316210.0001263049213530.3101201142760.0446037784623-0.04471721906990.2432996141150.001128791158680.34681650045826.147748322925.138435660543.5290282752
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 3 through 69 )3 - 691 - 67
22chain 'A' and (resid 70 through 148 )70 - 14868 - 146
33chain 'A' and (resid 149 through 187 )149 - 187147 - 185
44chain 'A' and (resid 188 through 240 )188 - 240186 - 236
55chain 'A' and (resid 241 through 318 )241 - 318237 - 314
66chain 'A' and (resid 319 through 354 )319 - 354315 - 350
77chain 'A' and (resid 355 through 391 )355 - 391351 - 387

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