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- PDB-3bpn: Crystal structure of the IL4-IL4R-IL13Ra ternary complex -

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Basic information

Entry
Database: PDB / ID: 3bpn
TitleCrystal structure of the IL4-IL4R-IL13Ra ternary complex
Components
  • Interleukin-13 receptor alpha-1 chain
  • Interleukin-4
  • Interleukin-4 receptor alpha chain
KeywordsCytokine/Cytokine receptor / IL4 / IL13 / IL13R / IL4R / cytokine / receptor / B-cell activation / Glycoprotein / Growth factor / Secreted / Immune response / Membrane / Phosphoprotein / Transmembrane / Cytokine-Cytokine receptor COMPLEX
Function / homology
Function and homology information


interleukin-13 receptor complex / interleukin-4 receptor activity / production of molecular mediator involved in inflammatory response / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / negative regulation of complement-dependent cytotoxicity / positive regulation of cellular respiration / regulation of isotype switching ...interleukin-13 receptor complex / interleukin-4 receptor activity / production of molecular mediator involved in inflammatory response / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / negative regulation of complement-dependent cytotoxicity / positive regulation of cellular respiration / regulation of isotype switching / Interleukin-18 signaling / positive regulation of T-helper 2 cell differentiation / negative regulation of neuroinflammatory response / negative regulation of epithelial cell migration / positive regulation of T-helper 2 cell cytokine production / dendritic cell differentiation / neuroinflammatory response / interleukin-4-mediated signaling pathway / positive regulation of isotype switching to IgG isotypes / positive regulation of mast cell degranulation / macrophage activation / positive regulation of interleukin-13 production / myeloid dendritic cell differentiation / positive regulation of amyloid-beta clearance / activation of Janus kinase activity / type 2 immune response / T-helper 2 cell differentiation / positive regulation of macrophage activation / regulation of phosphorylation / positive regulation of MHC class II biosynthetic process / cytokine receptor activity / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / positive regulation of immunoglobulin production / positive regulation of myoblast fusion / positive regulation of ATP biosynthetic process / defense response to protozoan / negative regulation of osteoclast differentiation / cytokine binding / positive regulation of macroautophagy / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / regulation of immune response / centriolar satellite / immunoglobulin mediated immune response / negative regulation of endothelial cell apoptotic process / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of B cell proliferation / positive regulation of T cell proliferation / cholesterol metabolic process / B cell differentiation / T cell activation / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / negative regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / receptor complex / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / external side of plasma membrane / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / plasma membrane
Similarity search - Function
Interleukin-13 receptor subunit alpha-1, Ig-like domain / Interleukin-13 receptor subunit alpha Ig-like domain / Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Interleukin-4 / Interleukin 4 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site ...Interleukin-13 receptor subunit alpha-1, Ig-like domain / Interleukin-13 receptor subunit alpha Ig-like domain / Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Interleukin-4 / Interleukin 4 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Short hematopoietin receptor family 1 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Growth Hormone; Chain: A; - #10 / Growth Hormone; Chain: A; / Four-helical cytokine-like, core / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-4 / Interleukin-4 receptor subunit alpha / Interleukin-13 receptor subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsGarcia, K.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Molecular and Structural Basis of Cytokine Receptor Pleiotropy in the Interleukin-4/13 System.
Authors: Laporte, S.L. / Juo, Z.S. / Vaclavikova, J. / Colf, L.A. / Qi, X. / Heller, N.M. / Keegan, A.D. / Garcia, K.C.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-4
B: Interleukin-4 receptor alpha chain
C: Interleukin-13 receptor alpha-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2645
Polymers74,8213
Non-polymers4422
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
Unit cell
Length a, b, c (Å)61.640, 62.841, 115.125
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interleukin-4 / IL-4 / B-cell stimulatory factor 1 / BSF-1 / Lymphocyte stimulatory factor 1 / Binetrakin / Pitrakinra


Mass: 14989.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL4 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P05112
#2: Protein Interleukin-4 receptor alpha chain / IL-4R-alpha / CD124 antigen / Soluble interleukin-4 receptor alpha chain


Mass: 23470.332 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 27-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL4R, 582J2.1, IL4RA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P24394
#3: Protein Interleukin-13 receptor alpha-1 chain / IL-13R-alpha-1 / IL-13RA-1 / Cancer/testis antigen 19 / CT19 / CD213a1 antigen


Mass: 36361.715 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 29-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL13RA1, IL13R, IL13RA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P78552
#4: 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.: 2
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG8K, 0.1M cacodylate pH 6.5, 0.16M calcium acetate, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 17403 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1729 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→30 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.829 / SU B: 49.084 / SU ML: 0.426 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30437 875 5 %RANDOM
Rwork0.23455 ---
obs0.23801 16508 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.635 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å23 Å2
2---0.68 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 3.02→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 28 52 5094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225154
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.9447026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0445615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12724.435239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16615855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7781526
X-RAY DIFFRACTIONr_chiral_restr0.0710.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023895
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.22277
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23469
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0690.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6551.53188
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95825062
X-RAY DIFFRACTIONr_scbond_it1.21932271
X-RAY DIFFRACTIONr_scangle_it1.7744.51964
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.02→3.096 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 54 -
Rwork0.337 1174 -
obs--96.47 %
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)
13.00880.4038-0.42713.18951.6725.59420.33730.3304-0.009-0.3341-0.0491-0.0094-0.1503-0.3822-0.2882-0.0390.20160.0414-0.1280.0753-0.105518.9404-10.721619.1555
25.3043-3.305-0.98585.96840.92880.20850.14710.38540.3166-0.3536-0.22170.03210.1161-0.01070.07460.08510.3080.10970.01530.1596-0.1386-2.051311.523423.9875
31.76080.2115-2.29221.8506-1.02775.4340.158-0.0068-0.0278-0.00760.01650.2287-0.3151-0.5635-0.1745-0.15990.15580.01340.09220.0963-0.0643-3.9383-7.867849.1845
43.59460.7325-2.19546.4239-2.89797.06410.15210.55490.23-0.72650.00880.2272-0.0314-0.7223-0.16090.05460.16370.0216-0.0645-0.0799-0.111533.5381-27.68856.8606
53.69130.1942-0.26912.07011.33093.9688-0.02520.08330.102-0.21080.0198-0.0739-0.05650.0250.0054-0.070.03090.0098-0.14340.028-0.086934.4577-37.844735.0465
62.8848-0.9397-2.76691.12291.50415.72560.11940.00350.02640.042-0.12350.0293-0.0874-0.17060.0041-0.0867-0.0101-0.0265-0.1207-0.0135-0.057715.3499-17.526353.1435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1283 - 128
2X-RAY DIFFRACTION2BB0 - 943 - 97
3X-RAY DIFFRACTION3BB95 - 19898 - 201
4X-RAY DIFFRACTION4CC30 - 1212 - 93
5X-RAY DIFFRACTION5CC122 - 22394 - 195
6X-RAY DIFFRACTION6CC224 - 338196 - 310

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