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- PDB-6u6u: IL36R extracellular domain in complex with BI655130 Fab -

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Basic information

Entry
Database: PDB / ID: 6u6u
TitleIL36R extracellular domain in complex with BI655130 Fab
Components
  • (BI00655130 Fab ...) x 2
  • Interleukin-1 receptor-like 2
KeywordsCYTOKINE / IL36R
Function / homology
Function and homology information


interleukin-1, type I, activating receptor activity / Interleukin-36 pathway / interleukin-1 receptor activity / Interleukin-38 signaling / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of T cell differentiation / plasma membrane => GO:0005886 / cellular response to cytokine stimulus ...interleukin-1, type I, activating receptor activity / Interleukin-36 pathway / interleukin-1 receptor activity / Interleukin-38 signaling / NADP+ nucleosidase activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of T cell differentiation / plasma membrane => GO:0005886 / cellular response to cytokine stimulus / cellular defense response / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / regulation of inflammatory response / inflammatory response / innate immune response / signal transduction / plasma membrane
Similarity search - Function
Interleukin-1 receptor type 1 / Interleukin-1 receptor type I/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 ...Interleukin-1 receptor type 1 / Interleukin-1 receptor type I/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 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsLarson, E.T. / Farrow, N.A.
CitationJournal: Protein Sci. / Year: 2020
Title: X-ray crystal structure localizes the mechanism of inhibition of an IL-36R antagonist monoclonal antibody to interaction with Ig1 and Ig2 extra cellular domains.
Authors: Larson, E.T. / Brennan, D.L. / Hickey, E.R. / Ganesan, R. / Kroe-Barrett, R. / Farrow, N.A.
History
DepositionAug 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)70,4786
Polymers69,8093
Non-polymers6693
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-37 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.698, 70.663, 233.268
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / IL1R-rp2


Mass: 22387.570 Da / Num. of mol.: 1 / Fragment: residues 20-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RL2, IL1RRP2 / Production host: Homo sapiens (human) / References: UniProt: Q9HB29

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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) / Production host: Cricetulus griseus (Chinese hamster)
#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) / Production host: Cricetulus griseus (Chinese hamster)

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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: isolated from a genetically manipulated source
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 , 2 types, 190 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.58 Å3/Da / Density % sol: 65.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Na3C6H5O7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→116.63 Å / Num. obs: 45094 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 47.97 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 12.7
Reflection shellResolution: 2.31→2.318 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.921 / Mean I/σ(I) obs: 2 / Num. unique obs: 45094 / Rsym value: 0.921 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
d*TREKdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G0Y

1g0y


Resolution: 2.31→36.99 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.1
RfactorNum. reflection% reflection
Rfree0.2021 2280 5.07 %
Rwork0.179 --
obs0.1802 44981 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.86 Å2 / Biso mean: 55.7426 Å2 / Biso min: 25.36 Å2
Refinement stepCycle: final / Resolution: 2.31→36.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 43 192 5135
Biso mean--82.32 50.14 -
Num. residues----632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095180
X-RAY DIFFRACTIONf_angle_d1.0877044
X-RAY DIFFRACTIONf_chiral_restr0.043791
X-RAY DIFFRACTIONf_plane_restr0.006899
X-RAY DIFFRACTIONf_dihedral_angle_d13.4861858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3101-2.36030.29471450.2722618
2.3603-2.41520.30321230.26122637
2.4152-2.47560.30591270.25692637
2.4756-2.54250.28321590.24462630
2.5425-2.61730.28161500.22592627
2.6173-2.70180.29541420.22932611
2.7018-2.79830.27961420.23372648
2.7983-2.91030.2391480.22412650
2.9103-3.04270.25941250.22942665
3.0427-3.2030.26051560.21442661
3.203-3.40360.2241480.19322628
3.4036-3.66620.17221370.17512675
3.6662-4.03470.16551380.15252706
4.0347-4.61760.15771410.12272691
4.6176-5.8140.12361490.13212743
5.814-36.990.20691500.17112874
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)
10.5952-0.1461-0.09030.3498-0.10461.38690.00510.2032-0.09920.06790.11-0.0240.2898-0.11960.01110.2204-0.0332-0.02730.3157-0.01280.30494.8829.6315.368
20.78930.08770.00190.8747-0.48250.94870.01210.2910.0242-0.00150.1466-0.0734-0.4384-0.04290.0010.28920.00740.04190.42470.0280.37672.87525.8738.077
30.455-0.6147-0.61282.59391.6930.96370.0418-0.14810.08020.31540.1988-0.31140.1420.33410.00290.47440.0279-0.07050.342-0.01920.397310.92724.72858.611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND ( RESID 1:221 OR RESID 301:301 ) )H1 - 221
2X-RAY DIFFRACTION1( CHAIN H AND ( RESID 1:221 OR RESID 301:301 ) )H301
3X-RAY DIFFRACTION2( CHAIN L AND RESID 1:214 )L1 - 214
4X-RAY DIFFRACTION3( CHAIN R AND ( RESID 21:217 OR RESID 301:303 ) )R21 - 217
5X-RAY DIFFRACTION3( CHAIN R AND ( RESID 21:217 OR RESID 301:303 ) )R301 - 303

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