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- PDB-4hwb: Crystal structure of ectodomain 3 of the IL-13 receptor alpha 1 i... -

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Basic information

Entry
Database: PDB / ID: 4hwb
TitleCrystal structure of ectodomain 3 of the IL-13 receptor alpha 1 in complex with a human neutralizing monoclonal antibody fragment
Components
  • Fab heavy chain
  • Fab light chain
  • Interleukin-13 receptor subunit alpha-1
KeywordsIMMUNE SYSTEM / Fab / FNIII / cytokine signaling
Function / homology
Function and homology information


interleukin-13 receptor complex / erythropoietin receptor activity / cytokine receptor activity / cytokine binding / cytokine-mediated signaling pathway / Interleukin-4 and Interleukin-13 signaling / cell surface receptor signaling pathway / receptor complex / external side of plasma membrane / positive regulation of cell population proliferation / plasma membrane
Similarity search - Function
Interleukin-13 receptor subunit alpha-1, Ig-like domain / Interleukin-13 receptor subunit alpha Ig-like domain / 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 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins ...Interleukin-13 receptor subunit alpha-1, Ig-like domain / Interleukin-13 receptor subunit alpha Ig-like domain / 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 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-13 receptor subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsXu, Y.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal structure of ectodomain 3 of the IL-13 receptor alpha 1 in complex with a human neutralizing monoclonal antibody fragment
Authors: Redpath, N.T. / Xu, Y. / Wilson, N.J. / Fabri, L.J. / Baca, M. / Andrews, A.E. / Braley, H. / Lu, P. / Ireland, C. / Ernst, R.E. / Woods, A. / Forrest, G. / An, Z. / Zaller, D.M. / Strohl, W. ...Authors: Redpath, N.T. / Xu, Y. / Wilson, N.J. / Fabri, L.J. / Baca, M. / Andrews, A.E. / Braley, H. / Lu, P. / Ireland, C. / Ernst, R.E. / Woods, A. / Forrest, G. / An, Z. / Zaller, D.M. / Strohl, W.R. / Luo, C.S. / Czabotar, P.E. / Garrett, T.P. / Hilton, D.J. / Nash, A.D. / Zhang, J.G. / Nicola, N.A.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other
Revision 1.2Jul 24, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-13 receptor subunit alpha-1
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,41121
Polymers62,1253
Non-polymers2,28518
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-121 kcal/mol
Surface area27080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.480, 123.480, 181.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Interleukin-13 receptor subunit alpha-1 / IL-13 receptor subunit alpha-1 / IL-13R subunit alpha-1 / IL-13R-alpha-1 / IL-13RA1 / Cancer/testis ...IL-13 receptor subunit alpha-1 / IL-13R subunit alpha-1 / IL-13R-alpha-1 / IL-13RA1 / Cancer/testis antigen 19 / CT19


Mass: 14650.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL13RA1, IL13R, IL13RA / Production host: Escherichia coli (E. coli) / References: UniProt: P78552

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fab heavy chain


Mass: 24342.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab light chain


Mass: 23132.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 95 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 5.57 Å3/Da / Density % sol: 77.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.6-2.0 M Li2SO4 0.1M CHES pH9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. all: 43581 / Num. obs: 42824 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 44.57 Å2
Reflection shellResolution: 2.61→2.76 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERMRphasing
BUSTER2.10.0refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→47.17 Å / Cor.coef. Fo:Fc: 0.9194 / Cor.coef. Fo:Fc free: 0.9074 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 2148 5.03 %RANDOM
Rwork0.1967 ---
obs0.1981 42736 98.55 %-
Displacement parametersBiso mean: 70.44 Å2
Baniso -1Baniso -2Baniso -3
1--5.8558 Å20 Å20 Å2
2---5.8558 Å20 Å2
3---11.7116 Å2
Refine analyzeLuzzati coordinate error obs: 0.441 Å
Refinement stepCycle: LAST / Resolution: 2.61→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4071 0 130 77 4278
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014297HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.275869HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1391SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes612HARMONIC5
X-RAY DIFFRACTIONt_it4297HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion552SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4547SEMIHARMONIC4
LS refinement shellResolution: 2.61→2.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3213 135 4.34 %
Rwork0.2864 2973 -
all0.288 3108 -
obs--98.55 %
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)
11.44950.0437-0.05771.933-0.90186.99850.00250.0160.11670.111-0.0572-0.188-0.1910.19250.05470.0058-0.00660.0223-0.05170.0204-0.1709-2.8357-70.113771.1765
23.7150.21480.10313.62920.44621.98160.0963-0.5396-0.53020.2936-0.0665-0.13110.5279-0.3715-0.02980.1887-0.152-0.0453-0.01040.0351-0.304-12.2148-93.190497.1126
33.13582.2937-0.53383.96780.32543.5984-0.1530.3695-0.2297-0.22260.03440.03270.5442-0.54420.11860.2997-0.1520.030.1407-0.0101-0.304-11.444-87.844559.9901
45.88332.5555-1.74855.18811.40664.28320.0796-0.4240.2104-0.1342-0.01470.52890.1386-0.4813-0.065-0.0706-0.1520.03530.01020.0317-0.3003-27.4323-95.187590.7008
52.82891.3566-0.09812.08222.55713.2168-0.0828-0.20380.03350.14130.03850.1335-0.05720.18780.04430.1432-0.1514-0.12730.15350.151-0.25399.9214-49.516952.0771
65.4976-2.9104-0.74152.72571.93633.3587-0.00660.0792-0.1793-0.1422-0.0472-0.10110.50490.35590.05380.29630.1520.04040.08030.1407-0.3046.0178-79.322143.5446
70-0.2961-2.23540.9711-1.82223.0066-0.0113-0.10780.05990.0501-0.0160.0558-0.18820.06270.0273-0.02120.029-0.10330.18650.1098-0.2987-4.332-54.507953.862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|1 - H|119 }H1 - 119
2X-RAY DIFFRACTION2{ H|120 - H|220 }H120 - 220
3X-RAY DIFFRACTION3{ L|1 - L|104 }L1 - 104
4X-RAY DIFFRACTION4{ L|105 - L|211 }L105 - 211
5X-RAY DIFFRACTION5{ A|200 - A|231 }A200 - 231
6X-RAY DIFFRACTION6{ A|232 - A|291 }A232 - 291
7X-RAY DIFFRACTION7{ A|292 - A|310 }A292 - 310

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