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- PDB-3lb6: The structure of IL-13 in complex with IL-13Ralpha2 -

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Basic information

Entry
Database: PDB / ID: 3lb6
TitleThe structure of IL-13 in complex with IL-13Ralpha2
Components
  • (Interleukin-13 receptor subunit alpha- ...) x 2
  • (Interleukin-13) x 2
Keywordssignaling protein/signaling protein / cytokine / receptor / decoy / decoy receptor / Glycoprotein / Secreted / signaling protein-signaling protein complex
Function / homology
Function and homology information


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 / negative regulation of immunoglobulin production / regulation of proton transport / positive regulation of connective tissue growth factor production / negative regulation of complement-dependent cytotoxicity / negative regulation of mast cell degranulation / Interleukin-18 signaling ...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 / negative regulation of immunoglobulin production / regulation of proton transport / positive regulation of connective tissue growth factor production / negative regulation of complement-dependent cytotoxicity / negative regulation of mast cell degranulation / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / macrophage activation / positive regulation of mast cell degranulation / positive regulation of macrophage activation / cytokine receptor activity / positive regulation of immunoglobulin production / cytokine binding / cellular response to cytokine stimulus / positive regulation of interleukin-10 production / immunoglobulin mediated immune response / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of release of sequestered calcium ion into cytosol / cytokine activity / positive regulation of protein secretion / positive regulation of smooth muscle cell proliferation / microglial cell activation / response to nicotine / cytokine-mediated signaling pathway / negative regulation of inflammatory response / cellular response to mechanical stimulus / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / response to ethanol / response to lipopolysaccharide / membrane => GO:0016020 / receptor complex / inflammatory response / immune response / external side of plasma membrane / positive regulation of gene expression / extracellular space / extracellular region / cytoplasm
Similarity search - Function
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 / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding ...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 / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / 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-13 receptor subunit alpha-2 / Interleukin-13 / Interleukin-13 receptor subunit alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsLupardus, P.J. / Garcia, K.C. / Birnbaum, M.E.
CitationJournal: Structure / Year: 2010
Title: Molecular basis for shared cytokine recognition revealed in the structure of an unusually high affinity complex between IL-13 and IL-13Ralpha2.
Authors: Lupardus, P.J. / Birnbaum, M.E. / Garcia, K.C.
History
DepositionJan 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 13, 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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-13
C: Interleukin-13 receptor subunit alpha-2
B: Interleukin-13
D: Interleukin-13 receptor subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,7248
Polymers117,2014
Non-polymers5234
Water55831
1
A: Interleukin-13
C: Interleukin-13 receptor subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8484
Polymers58,5872
Non-polymers2612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-13 kcal/mol
Surface area18290 Å2
MethodPISA
2
B: Interleukin-13
D: Interleukin-13 receptor subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8754
Polymers58,6142
Non-polymers2612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-14 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.370, 86.570, 166.788
Angle α, β, γ (deg.)90.00, 96.77, 90.00
Int Tables number5
Space group name H-MI121
Detailsthere are two IL-13/IL-13Ralpha2 complexes in the assymetric unit. IL-13 chain A associates with IL-13Ra2 chain C IL-13 chain B associates with IL-13Ra2 chain D

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Interleukin-13 / IL-13


Mass: 14333.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL13, NC30 / Plasmid: pACgp67 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35225
#3: Protein Interleukin-13


Mass: 14360.862 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL13, NC30 / Plasmid: pACgp67 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35225

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Interleukin-13 receptor subunit alpha- ... , 2 types, 2 molecules CD

#2: Protein Interleukin-13 receptor subunit alpha-2


Mass: 44253.293 Da / Num. of mol.: 1 / Mutation: R151Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pACgp67 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8K7E2, UniProt: Q14627*PLUS
#4: Protein Interleukin-13 receptor subunit alpha-2


Mass: 44253.297 Da / Num. of mol.: 1 / Mutation: R151Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pACgp67 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8K7E2, UniProt: Q14627*PLUS

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Sugars , 1 types, 2 molecules

#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


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

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Non-polymers , 2 types, 33 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES, pH 6.0, 200 mM CaCl2, 20% PEG-6000, and 4% v/v polypropylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→82.8 Å / Num. obs: 19978 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 68.6 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 7.6
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2 / Num. unique all: 2889 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IL-13 and IL-13Ralpha1

Resolution: 3.05→82.8 Å / SU ML: 0.45 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 954 5.09 %
Rwork0.2193 --
obs0.2219 18755 94.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.709 Å2 / ksol: 0.328 e/Å3
Refinement stepCycle: LAST / Resolution: 3.05→82.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6027 0 30 31 6088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126232
X-RAY DIFFRACTIONf_angle_d1.4268473
X-RAY DIFFRACTIONf_dihedral_angle_d16.8572158
X-RAY DIFFRACTIONf_chiral_restr0.085931
X-RAY DIFFRACTIONf_plane_restr0.0051060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0503-3.21110.34341100.30032294X-RAY DIFFRACTION85
3.2111-3.41230.31951370.26572395X-RAY DIFFRACTION90
3.4123-3.67580.30951390.22482545X-RAY DIFFRACTION94
3.6758-4.04570.25191510.21162549X-RAY DIFFRACTION95
4.0457-4.6310.2321460.17442629X-RAY DIFFRACTION98
4.631-5.83440.22171380.17412641X-RAY DIFFRACTION98
5.8344-82.84360.27941330.24492748X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.08080.02090.10.06610.04260.1437-0.0496-0.03420.0795-0.0057-0.05260.135-0.02790.04970.04460.1571-0.0583-0.06710.30340.25580.363915.9586-28.02774.0628
20.5872-0.648-0.31320.97470.09070.58670.06580.1818-0.0053-0.0436-0.20340.3335-0.20180.06810.14620.2009-0.0334-0.00980.37560.03580.2003
30.0509-0.1472-0.13810.8805-0.20691.4019-0.08580.33680.10.00030.14170.67180.0806-0.8164-0.07130.06220.038-0.04570.4772-0.02890.4694
40.3079-0.0028-0.09411.2164-0.85272.1966-0.02930.038-0.05-0.0085-0.10170.10390.21830.49150.11960.1642-0.00650.02760.146-0.0010.0831
50.17020.10770.3030.1810.06151.228-0.04630.1680.1235-0.0146-0.22220.08790.10610.49820.18820.07470.08410.03680.28190.12830.118
60.1047-0.28990.3512.1765-0.6641.21390.0551-0.1010.2665-0.0310.27060.2554-0.05290.018-0.29750.2209-0.0520.06581.0458-0.13450.3943
71.2409-0.5031-0.79072.3393-0.08340.61170.10910.3097-0.06910.1767-0.170.08440.0252-0.18310.06180.0892-0.07790.01410.14440.0120.2518
80.4355-0.3132-0.18541.145-0.62230.63030.1011-0.1728-0.1713-0.0489-0.06330.14660.03360.1334-0.00410.0162-0.0215-0.00310.11650.01240.0626
90.3018-0.14620.37880.538-0.14530.4523-0.06910.0184-0.1915-0.03310.2558-0.22030.0107-0.0473-0.18340.11760.0008-0.04070.1959-0.05210.2564
100.113-0.1452-0.1560.941-0.05550.2988-0.1506-0.06670.171-0.02820.02730.0746-0.0280.05120.12560.3230.3115-0.27350.39960.18730.7093
110.88940.6646-0.04860.6392-0.19450.4712-0.04520.33250.0039-0.16690.3191-0.0599-0.0173-0.0282-0.13070.2208-0.12010.1220.2791-0.15460.1451
121.0463-0.44320.7391.2592-0.86820.97610.27070.1983-0.0012-0.30730.28330.2520.2928-0.014-0.38410.51540.0018-0.09950.24980.13310.273
130.71190.1517-0.49960.0559-0.02050.6661-0.01730.2850.19460.10430.0755-0.0217-0.0368-0.0532-0.07470.55540.24120.02850.90030.12170.6085
140.04420.099-0.03161.2709-0.45610.375-0.079-0.1115-0.0522-0.01970.12030.30640.03390.0844-0.04730.12850.05950.01510.17070.06640.1841
150.3173-0.24850.22070.44530.11020.1834-0.0350.1555-0.0127-0.0242-0.0268-0.0477-0.0460.02160.0550.0506-0.01970.01250.12120.01070.0728
160.33130.2544-0.00182.71040.33320.0519-0.01850.10560.05350.91170.17220.1173-0.0619-0.1527-0.11760.4570.10830.07170.39250.02640.212
Refinement TLS groupSelection details: chain D and resid 275:305)

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