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- PDB-3bpo: Crystal structure of the IL13-IL4R-IL13Ra ternary complex -

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Basic information

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


interleukin-13 receptor complex / interleukin-4 receptor activity / interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / regulation of proton transport / positive regulation of connective tissue growth factor production / production of molecular mediator involved in inflammatory response / negative regulation of T-helper 1 cell differentiation ...interleukin-13 receptor complex / interleukin-4 receptor activity / interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / regulation of proton transport / positive regulation of connective tissue growth factor production / production of molecular mediator involved in inflammatory response / negative regulation of T-helper 1 cell differentiation / negative regulation of complement-dependent cytotoxicity / T-helper 1 cell differentiation / Interleukin-18 signaling / positive regulation of T-helper 2 cell differentiation / negative regulation of transforming growth factor beta production / interleukin-4-mediated signaling pathway / cytokine receptor binding / macrophage activation / positive regulation of mast cell degranulation / positive regulation of macrophage activation / T-helper 2 cell differentiation / cytokine receptor activity / positive regulation of myoblast fusion / cytokine binding / defense response to protozoan / cellular response to cytokine stimulus / positive regulation of interleukin-10 production / immunoglobulin mediated immune response / positive regulation of immunoglobulin production / centriolar satellite / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of release of sequestered calcium ion into cytosol / response to nicotine / cytokine activity / positive regulation of protein secretion / microglial cell activation / positive regulation of smooth muscle cell proliferation / negative regulation of inflammatory response / cytokine-mediated signaling pathway / cellular response to mechanical stimulus / positive regulation of cold-induced thermogenesis / response to ethanol / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / cell surface receptor signaling pathway / receptor complex / immune response / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytoplasm
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 / Interleukin-13 / Interleukin-13 / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / 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 / Interleukin-13 / Interleukin-13 / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / 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 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / 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 receptor subunit alpha / Interleukin-13 / Interleukin-13 receptor subunit alpha-1 / Interleukin-13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,6145
Polymers73,9683
Non-polymers6462
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.510, 58.169, 64.236
Angle α, β, γ (deg.)90.00, 100.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Interleukin 13 /


Mass: 14136.397 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL13 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q4VB50, UniProt: P35225*PLUS
#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

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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)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 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 , 1 types, 54 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 12% PEG8K, 8% ethlyene glycol, 0.1M ammonium citrate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 17289 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.9
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.2 / % possible all: 85.5

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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→30 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.84 / SU B: 58.148 / SU ML: 0.494 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.538 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31151 781 5 %RANDOM
Rwork0.25307 ---
obs0.25616 14726 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.236 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å2-3.56 Å2
2--3.51 Å20 Å2
3----3.51 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 42 54 4574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224668
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9466389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1815573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49424.293191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23215683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1661518
X-RAY DIFFRACTIONr_chiral_restr0.1060.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023527
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.22024
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23131
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2143
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5211.53017
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14124704
X-RAY DIFFRACTIONr_scbond_it0.71731962
X-RAY DIFFRACTIONr_scangle_it0.9564.51685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 61 -
Rwork0.335 1083 -
obs--99.83 %
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)
113.184-0.55220.86744.0526-1.8253.7980.09820.43660.45160.1552-0.4551-0.2992-0.08380.44260.3569-0.027-0.0446-0.0848-0.0070.2204-0.2261-11.8699-5.0395-28.1104
21.8094-0.5404-2.10654.208-4.42078.75440.0691-0.28630.11860.2844-0.4765-0.3349-0.69211.14310.4074-0.1335-0.1726-0.23630.25030.338-0.0428-8.985512.7601-53.2699
37.70172.30761.94053.35910.64064.4637-0.00480.23320.1463-0.1322-0.2976-0.01120.3858-0.32370.3024-0.18930.08840.08590.06910.1683-0.1719-33.4379-6.7293-58.4433
413.75035.22380.19245.60941.67074.05440.0104-0.02560.02830.2875-0.2445-0.5767-0.08410.57620.2342-0.08770.0165-0.1948-0.00030.2709-0.1299-0.7675-22.6389-11.179
53.634-0.63561.19132.7703-0.01324.76280.0211-0.01850.02880.1856-0.1369-0.1704-0.01240.14230.1158-0.0849-0.0184-0.0614-0.09070.0835-0.1437-27.8263-32.0621-17.1976
67.68750.17243.66442.0776-0.32425.07820.13830.37560.2470.0795-0.35370.06460.1705-0.01760.2154-0.09580.0607-0.0309-0.09540.0409-0.1459-42.9261-13.7363-40.6313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1122 - 113
2X-RAY DIFFRACTION2BB-1 - 952 - 98
3X-RAY DIFFRACTION3BB96 - 19699 - 199
4X-RAY DIFFRACTION4CC32 - 1214 - 93
5X-RAY DIFFRACTION5CC122 - 22894 - 200
6X-RAY DIFFRACTION6CC229 - 342201 - 314

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