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- PDB-9eth: Complex structure of IL-36R D1-D2 domain with 36R-P192 and BI6551... -

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Basic information

Entry
Database: PDB / ID: 9eth
TitleComplex structure of IL-36R D1-D2 domain with 36R-P192 and BI655130 Fab
Components
  • (BI00655130 Fab ...) x 2
  • ACE-PHE-VAL-GLU-5CW-3PN-TRP-ASP-TYR-VAL-CHG-6G5-SER-GLU-CYS-NH2
  • 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
Interleukin-1 receptor-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
P: ACE-PHE-VAL-GLU-5CW-3PN-TRP-ASP-TYR-VAL-CHG-6G5-SER-GLU-CYS-NH2
R: Interleukin-1 receptor-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,73617
Polymers73,0934
Non-polymers2,64313
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-109 kcal/mol
Surface area28820 Å2
Unit cell
Length a, b, c (Å)54.64, 175.35, 191.01
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11H-301-

SO4

21H-304-

NA

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Components

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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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Protein/peptide / Protein , 2 types, 2 molecules PR

#3: Protein/peptide ACE-PHE-VAL-GLU-5CW-3PN-TRP-ASP-TYR-VAL-CHG-6G5-SER-GLU-CYS-NH2


Mass: 2044.097 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Cyclic peptide, chemically synthesized, ligand/inhibitor of interest
Source: (synth.) synthetic construct (others)
#4: 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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Sugars , 3 types, 3 molecules

#5: 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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-1/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#9: 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 , 4 types, 163 molecules

#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric acid pH5 3.1 M Ammonium sulfate

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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: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 36731 / % possible obs: 88.8 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.031 / Rrim(I) all: 0.1 / Net I/σ(I): 14.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.226 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1837 / CC1/2: 0.746 / Rpim(I) all: 0.394 / Rrim(I) all: 1.289 / % possible all: 47

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→32.29 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.291 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.292 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.214
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 1781 -RANDOM
Rwork0.212 ---
obs0.2132 36718 88.8 %-
Displacement parametersBiso mean: 59.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.9174 Å20 Å20 Å2
2--2.4806 Å20 Å2
3----0.5632 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.3→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4904 0 164 153 5221
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075216HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.947140HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1710SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes868HARMONIC5
X-RAY DIFFRACTIONt_it5216HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion717SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3913SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion15.89
LS refinement shellResolution: 2.3→2.33 Å
RfactorNum. reflection% reflection
Rfree0.296 42 -
Rwork0.2714 --
obs0.2728 735 41.14 %
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)
17.8925-3.5208-4.53510.7921-2.068813.60630.2370.0344-0.29240.03440.1548-0.2218-0.2924-0.2218-0.39170.16760.01560.1446-0.145-0.0237-0.08970.628-34.587742.9917
21.68180.96730.58652.8779-0.09511.5122-0.145-0.02630.2464-0.0263-0.05820.38580.24640.38580.20320.02720.07070.09040.05590.0245-0.174712.26-30.56533.3325
31.0946-1.44850.24641.8439-0.95560.64780.03360.3434-0.16690.3434-0.08020.1709-0.16690.17090.0467-0.008-0.11340.00120.0907-0.0120.01640.37419.585416.5535
42.1101-2.4580.90693.9708-0.82850.9149-0.0464-0.2191-0.0074-0.21910.3234-0.0435-0.0074-0.0435-0.277-0.1452-0.11750.013-0.0380.14760.0809-16.93495.262611.6259
50-0.28060.86890.33510.646400.0032-0.012-0.0606-0.0120.0539-0.0784-0.0606-0.0784-0.05710.60380.0784-0.3040.4197-0.3040.59121.6734-4.333453.0185
601.57822.627400.74481.910.0012-0.1753-0.0085-0.1753-0.0403-0.3769-0.0085-0.37690.03910.17590.0858-0.02090.0360.01620.5835-7.8672-33.198427.1422
74.0255-1.46612.234514.9377-0.278514.0294-0.04590.69990.13950.69990.14830.34940.13950.3494-0.10240.47980.250.1027-0.12070.0783-0.214111.636-47.253549.054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ P|* }P0 - 15
2X-RAY DIFFRACTION2{ R|21-217 }R21 - 217
3X-RAY DIFFRACTION3{ H|* }H1 - 220
4X-RAY DIFFRACTION4{ L|* }L1 - 212
5X-RAY DIFFRACTION5{ R|301 }R301
6X-RAY DIFFRACTION6{ B|* }B1 - 2
7X-RAY DIFFRACTION7{ C|* }C1 - 6

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