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- PDB-7szl: Crystal structure of the Toll/interleukin-1 receptor domain of hu... -

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Basic information

Entry
Database: PDB / ID: 7szl
TitleCrystal structure of the Toll/interleukin-1 receptor domain of human IL-1R10 (IL-1RAPL2)
ComponentsX-linked interleukin-1 receptor accessory protein-like 2
KeywordsMEMBRANE PROTEIN / TIR domain / Interleukin-1 receptor / IMMUNE SYSTEM
Function / homology
Function and homology information


interleukin-1, type II, blocking receptor activity / interleukin-1 receptor activity / Receptor-type tyrosine-protein phosphatases / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / regulation of presynapse assembly / central nervous system development / membrane => GO:0016020 / glutamatergic synapse / plasma membrane
Similarity search - Function
Interleukin-1 receptor type II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / Immunoglobulin domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Interleukin-1 receptor type II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / Immunoglobulin domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
X-linked interleukin-1 receptor accessory protein-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNimma, S. / Gu, W. / Manik, M.K. / Ve, T. / Nanson, J.D. / Kobe, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL180100109, FT200100572 Australia
National Health and Medical Research Council (NHMRC, Australia)1107804, 1160570, 1071659 Australia
CitationJournal: Febs Lett. / Year: 2022
Title: Crystal structure of the Toll/interleukin-1 receptor (TIR) domain of IL-1R10 provides structural insights into TIR domain signalling.
Authors: Nimma, S. / Gu, W. / Manik, M.K. / Ve, T. / Nanson, J.D. / Kobe, B.
History
DepositionNov 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: X-linked interleukin-1 receptor accessory protein-like 2


Theoretical massNumber of molelcules
Total (without water)18,9201
Polymers18,9201
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.655, 50.655, 181.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein X-linked interleukin-1 receptor accessory protein-like 2 / IL-1 receptor accessory protein-like 2 / IL-1-RAPL-2 / IL-1RAPL-2 / IL1RAPL-2 / IL1RAPL-2-related ...IL-1 receptor accessory protein-like 2 / IL-1-RAPL-2 / IL-1RAPL-2 / IL1RAPL-2 / IL1RAPL-2-related protein / IL-1R10


Mass: 18919.918 Da / Num. of mol.: 1 / Fragment: TIR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RAPL2, IL1R9 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NP60, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.08 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2.4 M sodium malonate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.3→38.88 Å / Num. obs: 11338 / % possible obs: 99.6 % / Redundancy: 24.8 % / Biso Wilson estimate: 64.98 Å2 / CC1/2: 1 / Net I/σ(I): 25.5
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 27 % / Num. unique obs: 1066 / CC1/2: 0.941 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T3G

1t3g


Resolution: 2.3→38.88 Å / SU ML: 0.2077 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2613 572 5.08 %
Rwork0.2385 10692 -
obs0.2396 11264 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 0 2 1285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231309
X-RAY DIFFRACTIONf_angle_d0.43171763
X-RAY DIFFRACTIONf_chiral_restr0.0409196
X-RAY DIFFRACTIONf_plane_restr0.0023217
X-RAY DIFFRACTIONf_dihedral_angle_d7.8661803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.33381440.30272582X-RAY DIFFRACTION99.96
2.53-2.90.2811300.3052621X-RAY DIFFRACTION99.96
2.9-3.650.34041470.27562660X-RAY DIFFRACTION100
3.65-38.880.22711510.21232829X-RAY DIFFRACTION99.9
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)
17.391906236781.98326154826-1.377522809656.25160655152-1.744391077645.88922985051-0.0471482060150.0924939702003-0.551502956175-0.3934459679090.3886956604050.5802062468730.3898181129160.0275975135271-0.2217679420080.9735080855670.0103151723169-0.08955352914510.472029028713-0.001669462262720.639472753025-14.9941786685-13.9729803049-17.7058425975
23.06454746813-1.055007852822.495699882643.88875234639-3.399624042758.708963450720.413479745630.567583343015-0.656560998109-0.4929095768750.0475662591254-0.02456805986331.789494464121.21948770533-0.5408327333950.9415979659220.267695984961-0.03422071828570.801921260946-0.1121190157030.696226396937-2.27204270048-13.5573447767-16.6904827174
37.690433282061.275237903174.222378916956.44554108283-0.62926931544.998945403380.619773921084-0.410666286445-0.315508241232-0.5612153305530.1637783571140.2782340658720.286368475839-0.497702718725-0.4590380074570.518373958574-0.0974211817309-0.0849046003680.4691118188530.04757209240660.493539117645-10.283327917-7.99516635243-8.88185178346
43.9266948327-2.496549056053.76783914632.15153530127-2.677431013224.21264215952-0.2561268043870.4421089331560.1756189731280.0846959755051-0.659060824194-0.931767596719-0.5072021285250.7122606867930.2951065542350.701467648572-0.0796484055915-0.05684789123510.6750248631340.1049320685290.7980255733080.415488400142-1.03264515988-6.94829827756
53.84592067297-0.3447429940122.241688525128.34927522699-2.279057972224.26372327918-0.240848101939-0.3655227120.5831411687170.004796966197580.442050357450.928023255664-0.233745039174-1.20614801228-0.2156117781860.6066551685970.0434669159559-0.0572028742310.6834434620370.07133126727980.663954614105-15.8739748514-0.68060893553-6.24852851948
64.856038856521.966141314981.399163387835.27781631518-0.7156083541278.9002196086-0.4487483306530.4191756894641.14089417705-0.7743948519610.1662261467510.944197856416-0.818215018833-0.07731165557970.2524379878840.8427824265980.0216917517133-0.1066337039570.4324906746180.01272350577550.558166255011-18.6075007743-1.49929168117-21.302980173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 127 )
6X-RAY DIFFRACTION6chain 'A' and (resid 128 through 159 )

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