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- PDB-3qt2: Structure of a cytokine ligand-receptor complex -

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Basic information

Entry
Database: PDB / ID: 3qt2
TitleStructure of a cytokine ligand-receptor complex
Components
  • Interleukin-5
  • Interleukin-5 receptor subunit alpha
KeywordsPROTEIN BINDING/IMMUNE SYSTEM / cytokine type I receptor fold / fibronectin type III modules / four-helical bundle / Cytokine / Ligand-receptor complex / membrane / PROTEIN BINDING-IMMUNE SYSTEM complex
Function / homology
Function and homology information


interleukin-5 receptor activity / regulation of interleukin-5 production / positive regulation of eosinophil differentiation / interleukin-5 receptor binding / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / inflammatory response to antigenic stimulus / cytokine receptor activity / positive regulation of podosome assembly / positive regulation of immunoglobulin production ...interleukin-5 receptor activity / regulation of interleukin-5 production / positive regulation of eosinophil differentiation / interleukin-5 receptor binding / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / inflammatory response to antigenic stimulus / cytokine receptor activity / positive regulation of podosome assembly / positive regulation of immunoglobulin production / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / positive regulation of B cell proliferation / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / RAF/MAP kinase cascade / receptor complex / immune response / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / signal transduction / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Interleukin-5 / Interleukin 5 / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / 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. ...Interleukin-5 / Interleukin 5 / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / 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 / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-D-glucopyranose / Interleukin-5 / Interleukin-5 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsMueller, T.D. / Patino, E. / Kotzsch, A. / Saremba, S. / Nickel, J. / Schmitz, W. / Sebald, W.
CitationJournal: Structure / Year: 2011
Title: Structure Analysis of the IL-5 Ligand-Receptor Complex Reveals a Wrench-like Architecture for IL-5Ralpha.
Authors: Patino, E. / Kotzsch, A. / Saremba, S. / Nickel, J. / Schmitz, W. / Sebald, W. / Mueller, T.D.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Jul 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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-5 receptor subunit alpha
C: Interleukin-5
D: Interleukin-5
B: Interleukin-5 receptor subunit alpha
E: Interleukin-5
F: Interleukin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,90813
Polymers125,7096
Non-polymers1,1997
Water99155
1
A: Interleukin-5 receptor subunit alpha
C: Interleukin-5
D: Interleukin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5137
Polymers62,8553
Non-polymers6594
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-60 kcal/mol
Surface area27020 Å2
MethodPISA
2
B: Interleukin-5 receptor subunit alpha
E: Interleukin-5
F: Interleukin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3956
Polymers62,8553
Non-polymers5403
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-65 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.084, 61.633, 142.113
Angle α, β, γ (deg.)90.00, 99.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interleukin-5 receptor subunit alpha / IL-5 receptor subunit alpha / IL-5R subunit alpha / IL-5R-alpha / IL-5RA / CDw125


Mass: 36117.719 Da / Num. of mol.: 2 / Mutation: C66A, K72M, L138M, K167M, L234M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL5R, IL5RA / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01344
#2: Protein
Interleukin-5 / IL-5 / B-cell differentiation factor I / Eosinophil differentiation factor / T-cell replacing factor / TRF


Mass: 13368.470 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL5 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05113
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsISOFORM 2 (IDENTIFIER: Q01344-2), 333-335: NDE -> FSR, 336-420: MISSING

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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: 2.92 Å3/Da / Density % sol: 57.93 %
Description: The entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% (w/v) PEG 20000, 0.1M MOPS pH 6.5, 20% (w/v) glucose, 2.5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9079, 0.9795, 0.9797
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2006
RadiationMonochromator: Double xtal Si(111) fixed-exit monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.90791
20.97951
30.97971
ReflectionResolution: 2.55→140.03 Å / Num. all: 91896 / Num. obs: 91854 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.53 % / Rsym value: 0.06 / Net I/σ(I): 8.2
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 2.53 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.9 / Num. unique all: 8715 / % possible all: 100

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.2.0005refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.55→42.02 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 16.291 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.299
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: The entry contains Friedel pairs in F_Plus/Minus columns. The sf file includes data of a three wavelength dataset. Only the reflections for the inflection wavelength are only to 2.8A ...Details: The entry contains Friedel pairs in F_Plus/Minus columns. The sf file includes data of a three wavelength dataset. Only the reflections for the inflection wavelength are only to 2.8A resolution, the dataset for the wavelength for remote and peak are up to 2.55A resolution.
RfactorNum. reflection% reflectionSelection details
Rfree0.26442 2424 5.1 %RANDOM
Rwork0.20723 ---
all0.21025 ---
obs0.21025 91854 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 80.658 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å20 Å20.44 Å2
2--4.74 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.55→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8446 0 80 55 8581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228723
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.96111855
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34151045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16424.378402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.078151526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6561552
X-RAY DIFFRACTIONr_chiral_restr0.1240.21365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026470
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2970.33689
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3430.55970
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.5472
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.357
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0661.55358
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83328543
X-RAY DIFFRACTIONr_scbond_it2.64633792
X-RAY DIFFRACTIONr_scangle_it4.1274.53312
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 171 -
Rwork0.322 3296 -
obs--99.48 %
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)
15.28822.63470.45996.7689-0.3684.02810.224-0.42560.02820.3712-0.1969-0.1405-0.12650.2397-0.0272-0.2992-0.0324-0.058-0.35450.0351-0.31737.649230.504596.3312
26.1955-2.4079-4.93611.91592.48315.65690.11660.1305-0.05670.0362-0.14660.3382-0.0541-0.71660.03-0.1551-0.00440.0219-0.41060.0167-0.14048.176742.130192.4293
38.7885-2.6248-3.36272.47831.31635.56760.25221.12840.4916-0.5144-0.14090.0373-0.1746-0.8315-0.1113-0.04660.0022-0.0319-0.28280.0668-0.164417.474641.094977.6349
43.71461.5569-3.40371.3508-0.56875.51720.2062-0.2040.3772-0.09090.0329-0.1507-0.610.7422-0.2391-0.06590.03080.0661-0.4295-0.0013-0.078880.676310.2118114.9762
53.75770.7745-3.7232.7826-1.16846.79360.2632-0.9390.28310.3974-0.143-0.1255-0.44810.9213-0.1202-0.0866-0.0181-0.0579-0.2889-0.0571-0.138374.02399.2507130.9698
65.8860.24332.11263.0272-0.28137.70430.3533-0.3126-0.73310.3801-0.09290.04371.0493-0.7208-0.2604-0.1133-0.2645-0.0273-0.27620.0653-0.155418.97387.982290.6715
73.08231.06851.66463.18393.40848.4207-0.0060.4483-0.1979-0.2519-0.27060.321-0.0743-0.82150.2765-0.36070.0273-0.049-0.0315-0.1248-0.11695.744514.493560.056
86.5309-3.59010.73037.0536-0.09533.80730.20920.4680.0049-0.3563-0.11740.1174-0.1142-0.2694-0.0918-0.27160.0323-0.0492-0.3186-0.0171-0.340350.8118-1.201115.7485
97.2969-0.95911.33833.384-0.42664.49410.45030.5689-1.2011-0.4408-0.14840.25860.77650.2559-0.3018-0.05230.16-0.0732-0.339-0.1335-0.063570.3097-23.6138118.952
103.7904-1.52642.80674.3307-4.36528.9558-0.125-0.37820.01670.2322-0.2985-0.5812-0.07810.73630.4235-0.29030.0177-0.0061-0.12590.0815-0.163288.6611-17.0179146.373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 36
2X-RAY DIFFRACTION1A42 - 83
3X-RAY DIFFRACTION1A88 - 102
4X-RAY DIFFRACTION2C6 - 112
5X-RAY DIFFRACTION3D6 - 112
6X-RAY DIFFRACTION4E6 - 112
7X-RAY DIFFRACTION5F6 - 112
8X-RAY DIFFRACTION6A103 - 120
9X-RAY DIFFRACTION6A129 - 214
10X-RAY DIFFRACTION7A215 - 222
11X-RAY DIFFRACTION7A230 - 313
12X-RAY DIFFRACTION8B8 - 36
13X-RAY DIFFRACTION8B42 - 83
14X-RAY DIFFRACTION8B88 - 102
15X-RAY DIFFRACTION9B103 - 120
16X-RAY DIFFRACTION9B129 - 214
17X-RAY DIFFRACTION10B215 - 222
18X-RAY DIFFRACTION10B230 - 313

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