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- PDB-4kc3: Cytokine/receptor binary complex -

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Basic information

Entry
Database: PDB / ID: 4kc3
TitleCytokine/receptor binary complex
Components
  • Interleukin-1 receptor-like 1
  • Interleukin-33Interleukin 33
KeywordsIMMUNE SYSTEM / beta-trefoil / Ig-like domain
Function / homology
Function and homology information


interleukin-33 binding / interleukin-33 receptor binding / negative regulation of macrophage proliferation / positive regulation of CD86 production / positive regulation of CD80 production / positive regulation of cellular defense response / positive regulation of chemokine production => GO:0032722 / Interleukin-33 signaling / interleukin-33 receptor activity / positive regulation of MHC class I biosynthetic process ...interleukin-33 binding / interleukin-33 receptor binding / negative regulation of macrophage proliferation / positive regulation of CD86 production / positive regulation of CD80 production / positive regulation of cellular defense response / positive regulation of chemokine production => GO:0032722 / Interleukin-33 signaling / interleukin-33 receptor activity / positive regulation of MHC class I biosynthetic process / negative regulation of T-helper 1 type immune response / negative regulation of immunoglobulin production / interleukin-1 receptor activity / microglial cell activation involved in immune response / negative regulation of inflammatory response to wounding / negative regulation of leukocyte migration / microglial cell proliferation / interleukin-33-mediated signaling pathway / positive regulation of type 2 immune response / positive regulation of neuroinflammatory response / positive regulation of interleukin-5 production / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / type 2 immune response / positive regulation of macrophage activation / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / positive regulation of MHC class II biosynthetic process / cytokine receptor activity / positive regulation of interleukin-13 production / positive regulation of oligodendrocyte differentiation / positive regulation of nitric-oxide synthase biosynthetic process / macrophage differentiation / negative regulation of type II interferon production / positive regulation of immunoglobulin production / positive regulation of interleukin-4 production / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / transport vesicle / cytokine activity / positive regulation of cytokine production / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / protein import into nucleus / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / chromosome / gene expression / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / defense response to virus / membrane => GO:0016020 / Ub-specific processing proteases / immune response / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Interleukin-33 / Interleukin 33 / Interleukin-1 receptor type I/II / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 ...Interleukin-33 / Interleukin 33 / Interleukin-1 receptor type I/II / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-33 / Interleukin-1 receptor-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2702 Å
AuthorsLiu, X. / Wang, X.Q.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural insights into the interaction of IL-33 with its receptors.
Authors: Liu, X. / Hammel, M. / He, Y. / Tainer, J.A. / Jeng, U.S. / Zhang, L. / Wang, S. / Wang, X.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 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
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-33
B: Interleukin-1 receptor-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8765
Polymers53,2122
Non-polymers6643
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint3 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)329.924, 329.924, 43.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Interleukin-33 / Interleukin 33 / IL-33 / Interleukin-1 family member 11 / IL-1F11 / Nuclear factor from high endothelial venules / NF-HEV


Mass: 18155.857 Da / Num. of mol.: 1 / Fragment: UNP residues 112-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL33, C9orf26, IL1F11, NFHEV / Production host: Escherichia coli (E. coli) / References: UniProt: O95760
#2: Protein Interleukin-1 receptor-like 1 / Protein ST2


Mass: 35056.531 Da / Num. of mol.: 1 / Fragment: UNP residues 19-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RL1, DER4, ST2, T1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01638
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 12% PEG3350, 100 mM Sodium Malonate pH 4.5, 7% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.27→50 Å / Num. all: 14029 / Num. obs: 14000 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KLL and 1IRA

3kll

1ira


Resolution: 3.2702→32.007 Å / SU ML: 0.46 / σ(F): 0 / Phase error: 33.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2831 703 5.02 %
Rwork0.2384 --
obs0.2407 14000 99.79 %
all-14029 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2702→32.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 42 0 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113434
X-RAY DIFFRACTIONf_angle_d1.7244642
X-RAY DIFFRACTIONf_dihedral_angle_d20.4811260
X-RAY DIFFRACTIONf_chiral_restr0.121518
X-RAY DIFFRACTIONf_plane_restr0.006588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2702-3.52240.34471520.28522625X-RAY DIFFRACTION100
3.5224-3.87640.31581490.26262649X-RAY DIFFRACTION100
3.8764-4.4360.28361430.20512662X-RAY DIFFRACTION100
4.436-5.58410.22891410.22362658X-RAY DIFFRACTION100
5.5841-32.00870.29581180.24692703X-RAY DIFFRACTION99
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)
13.8348-0.7483-0.68385.1309-0.47113.5437-0.3597-0.5739-0.52130.44290.3974-0.4357-0.3846-0.03370.00011.35150.2251-0.01581.1346-0.05191.126946.7239-41.20217.5061
22.86971.51970.04525.27722.32713.57650.0130.26660.3243-0.22760.19960.3471-0.42480.22690.00021.51930.0522-0.00510.9489-0.15151.056239.1812-18.59928.7233
31.6353-0.5281-0.66810.80610.54061.9026-0.20050.3291-1.0933-0.98860.1212-0.40580.08220.48310.04061.20470.01410.25641.24-0.26381.819749.662-60.27982.2924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B and resid 21:186
3X-RAY DIFFRACTION3chain B and resid 194:299

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