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- PDB-9eti: Complex structure of IL-36R D1-D2 domain with 36R-D481 and BI6551... -

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Basic information

Entry
Database: PDB / ID: 9eti
TitleComplex structure of IL-36R D1-D2 domain with 36R-D481 and BI655130 Fab
Components
  • (BI00655130 Fab ...) x 2
  • Interleukin-1 receptor-like 2
KeywordsCYTOKINE / Inhibitor / Complex / Fab
Function / homology
Function and homology information


interleukin-1, type I, activating receptor activity / Interleukin-36 pathway / interleukin-1 receptor activity / Interleukin-38 signaling / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of T cell differentiation / cellular defense response / positive regulation of interleukin-6 production / regulation of inflammatory response ...interleukin-1, type I, activating receptor activity / Interleukin-36 pathway / interleukin-1 receptor activity / Interleukin-38 signaling / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of T cell differentiation / cellular defense response / positive regulation of interleukin-6 production / regulation of inflammatory response / cell surface receptor signaling pathway / inflammatory response / innate immune response / cell surface / signal transduction / plasma membrane
Similarity search - Function
Interleukin-1 receptor type 1 / Interleukin-1 receptor type I/II / Interleukin-1 receptor family / TIR domain / Immunoglobulin domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin subtype ...Interleukin-1 receptor type 1 / Interleukin-1 receptor type I/II / Interleukin-1 receptor family / TIR domain / Immunoglobulin domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / PHOSPHATE ION / Interleukin-1 receptor-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsScheufler, C. / Wirth, E. / Lehmann, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Discovery of selective low molecular weight interleukin-36 receptor antagonists by encoded library technologies.
Authors: Velcicky, J. / Cremosnik, G. / Scheufler, C. / Meier, P. / Wirth, E. / Felber, R. / Ramage, P. / Schaefer, M. / Kaiser, C. / Lehmann, S. / Kutil, R. / Singeisen, S. / Mueller-Ristig, D. / ...Authors: Velcicky, J. / Cremosnik, G. / Scheufler, C. / Meier, P. / Wirth, E. / Felber, R. / Ramage, P. / Schaefer, M. / Kaiser, C. / Lehmann, S. / Kutil, R. / Singeisen, S. / Mueller-Ristig, D. / Popp, S. / Cebe, R. / Lehr, P. / Kaupmann, K. / Erbel, P. / Rohn, T.A. / Giovannoni, J. / Dumelin, C.E. / Martiny-Baron, G.
History
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: BI00655130 Fab heavy chain
L: BI00655130 Fab light chain
R: Interleukin-1 receptor-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5417
Polymers71,0493
Non-polymers1,4924
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-27 kcal/mol
Surface area28120 Å2
Unit cell
Length a, b, c (Å)60.55, 69.94, 232.83
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules R

#3: Protein Interleukin-1 receptor-like 2 / IL-36 receptor / IL-36R / Interleukin-1 receptor-related protein 2 / IL-1Rrp2 / IL1R-rp2


Mass: 23626.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal Hexa-Histidine-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RL2, IL1RRP2 / Production host: Homo sapiens (human) / Strain (production host): HEK
References: UniProt: Q9HB29, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase

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Antibody , 2 types, 2 molecules HL

#1: Antibody BI00655130 Fab heavy chain


Mass: 23783.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HELA / Production host: Homo sapiens (human) / Strain (production host): HEK / Variant (production host): 293
#2: Antibody BI00655130 Fab light chain


Mass: 23638.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HELA / Production host: Homo sapiens (human) / Strain (production host): HEK / Variant (production host): 293

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Sugars , 2 types, 2 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 220 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-A1H62 / 4-[3-[[(1~{S})-1-(3-bromophenyl)-3-[2-(2-morpholin-4-ylethoxy)ethylamino]-3-oxidanylidene-propyl]carbamoyl]-1,4,6,7-tetrahydropyrazolo[4,3-c]pyridin-5-yl]-5-cyano-thieno[2,3-b]pyridine-2-carboxylic acid


Mass: 751.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H35BrN8O6S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium citrate tribasic dihydrate pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 34139 / % possible obs: 86.1 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.022 / Rrim(I) all: 0.069 / Net I/σ(I): 19.5
Reflection shellResolution: 2.4→2.52 Å / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1707 / CC1/2: 0.857 / Rpim(I) all: 0.301 / Rrim(I) all: 0.957 / % possible all: 32.6

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.74 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.293 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.305 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.211
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 1656 -RANDOM
Rwork0.189 ---
obs0.1904 34139 86.1 %-
Displacement parametersBiso mean: 58.98 Å2
Baniso -1Baniso -2Baniso -3
1-4.701 Å20 Å20 Å2
2---3.3876 Å20 Å2
3----1.3134 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 96 218 5144
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075064HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.956913HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1661SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes841HARMONIC5
X-RAY DIFFRACTIONt_it5064HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion682SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3831SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion14.83
LS refinement shellResolution: 2.4→2.45 Å
RfactorNum. reflection% reflection
Rfree0.3266 23 -
Rwork0.2526 --
obs0.2551 683 28.46 %
Refinement TLS params.

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)
10.9137-0.90260.82463.0338-2.09571.75050.11080.2997-0.0930.2997-0.0559-0.1948-0.093-0.1948-0.05490.12760.00350.0713-0.1091-0.0381-0.0888-10.7041-24.010458.2703
20.5645-0.13050.55480.12930.13362.5979-0.03570.1076-0.24470.10760.06930.1005-0.24470.1005-0.0336-0.0034-0.01560.0113-0.00170.0031-0.0263-5.3612-9.144115.8274
30.6821-0.3706-0.10610.8298-0.10343.3729-0.00840.0790.46330.0790.05690.13150.46330.1315-0.0485-0.0530.001-0.02480.0115-0.0712-0.1077-3.6531-25.68768.0615
412.8844.83095.78460-5.82081.70720.0688-0.4997-0.9387-0.49970.2797-1.0196-0.9387-1.0196-0.34850.11130.0741-0.08230.0112-0.00380.1557-18.7731-35.414559.0185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ R|* }R21 - 218
2X-RAY DIFFRACTION1{ R|* }R301 - 303
3X-RAY DIFFRACTION2{ H|* }H1 - 220
4X-RAY DIFFRACTION3{ L|* }L1 - 214
5X-RAY DIFFRACTION4{ I|* }I1

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