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- PDB-3va2: Crystal structure of human Interleukin-5 in complex with its alph... -

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Basic information

Entry
Database: PDB / ID: 3va2
TitleCrystal structure of human Interleukin-5 in complex with its alpha receptor
Components
  • Interleukin-5 receptor subunit alpha
  • Interleukin-5Interleukin 5
KeywordsCYTOKINE/CYTOKINE RECEPTOR / cytokine / eosinophilic / asthma / JAK/STAT / fibronectin III-like (Fn III) domain / canonical cytokine receptor homology module (CRM) / B cell growth / Ig secretion / eosinophils proliferation / cell surface / CYTOKINE-CYTOKINE RECEPTOR 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 / positive regulation of podosome assembly / cytokine receptor activity / cytokine binding ...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 / positive regulation of podosome assembly / cytokine receptor activity / cytokine binding / positive regulation of immunoglobulin production / 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 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 / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-5 / Interleukin-5 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.703 Å
AuthorsKusano, S. / Kukimoto-Niino, M. / Shirouzu, M. / Yokoyama, S.
CitationJournal: Protein Sci. / Year: 2012
Title: Structural basis of interleukin-5 dimer recognition by its alpha receptor
Authors: Kusano, S. / Kukimoto-Niino, M. / Hino, N. / Ohsawa, N. / Ikutani, M. / Takaki, S. / Sakamoto, K. / Hara-Yokoyama, M. / Shirouzu, M. / Takatsu, K. / Yokoyama, S.
History
DepositionDec 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-5
B: Interleukin-5
C: Interleukin-5 receptor subunit alpha


Theoretical massNumber of molelcules
Total (without water)63,1423
Polymers63,1423
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-59 kcal/mol
Surface area26690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.633, 88.680, 126.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Interleukin-5 / Interleukin 5 / IL-5 / B-cell differentiation factor I / Eosinophil differentiation factor / T-cell replacing factor / TRF


Mass: 13374.286 Da / Num. of mol.: 2 / Fragment: UNP residues 23-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL5 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P05113
#2: Protein Interleukin-5 receptor subunit alpha / / IL-5 receptor subunit alpha / IL-5R subunit alpha / IL-5R-alpha / IL-5RA / CDw125


Mass: 36393.727 Da / Num. of mol.: 1 / Fragment: ectodomain, UNP residues 21-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL5RA, IL5R / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q01344
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M Na HEPES, 22% (v/v) PEG 4000, 2% i-Propanol, 6% (w/v) 1,6-Hexanediol , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.703→50 Å / Num. obs: 18667 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.07 / Net I/σ(I): 22.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.8-2.96.80.3497.20.0641100
2.9-3.026.80.5527.50.0651100
3.02-3.156.80.8067.80.066199.9
3.15-3.326.81.3548.80.0691100
3.32-3.536.82.321120.073199.9
3.53-3.86.83.313.80.0761100
3.8-4.186.75.36919.70.0821100
4.18-4.796.69.09531.50.096199.9
4.79-6.036.58.40939.20.0881100
6.03-505.814.30359.10.218194.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.703→43.027 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 27.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2755 942 5.06 %random
Rwork0.2227 ---
obs0.2253 18615 99.44 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.279 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.0937 Å2-0 Å2-0 Å2
2---17.8849 Å2-0 Å2
3----10.0862 Å2
Refinement stepCycle: LAST / Resolution: 2.703→43.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 0 32 4235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034298
X-RAY DIFFRACTIONf_angle_d0.735829
X-RAY DIFFRACTIONf_dihedral_angle_d14.6591589
X-RAY DIFFRACTIONf_chiral_restr0.05666
X-RAY DIFFRACTIONf_plane_restr0.002741
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7032-2.84570.39431340.31762474100
2.8457-3.0240.30781460.28422497100
3.024-3.25740.331280.25592522100
3.2574-3.58510.32391370.24382493100
3.5851-4.10350.26741320.21652535100
4.1035-5.16860.26361390.17652551100
5.1686-43.03220.22891260.2219260197
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)
15.7566-1.02223.27896.7859-4.00599.161-0.59360.2257-0.3216-0.2542-0.45811.5173-1.9001-1.48570.8180.95270.3172-0.17410.971-0.30141.48723.065418.21632.2948
26.7385.3667-3.06345.2066-3.1034.3126-0.00230.95870.147-3.0334-0.3807-0.1709-1.8273-1.31960.34532.43950.0428-0.23610.7901-0.14331.631231.862526.1508-7.5312
38.8224-3.8951-0.43241.78510.50011.36930.59591.7741-0.2695-1.0274-0.5941-2.3143-2.77541.0190.34431.9376-0.40220.71231.3095-0.05831.793644.861319.8868-12.4886
43.43252.64611.15768.71495.34423.2469-0.70330.6944-0.7044-0.53360.19930.19760.60141.27170.5830.7329-0.05090.220.81570.10831.186435.62857.3276-6.9604
54.4471-5.29910.93817.99161.66454.5743-1.568-1.6259-1.6055-0.11070.7429-0.7051-2.30382.22680.72341.3849-0.38430.17921.23240.13991.520640.630924.9576-0.7069
67.43695.0657-2.33624.1902-3.66939.52360.1128-0.1099-0.01160.67420.0214-0.1467-0.83660.1126-0.19690.41950.0216-0.01110.538-0.0140.993131.652213.35975.02
78.43622.7223-4.97537.1484-0.72622.9596-0.4882-0.0381-0.3693-0.23150.29390.2368-0.0651-1.010.22290.6839-0.01410.00790.6478-0.03810.449324.2408-11.41415.7727
84.0783-3.97050.69353.94240.02422.2578-0.45221.04290.7482-0.6080.41330.76-0.93520.80750.57030.935-0.2025-0.08670.7098-0.06760.679324.2068-5.4556-10.7818
97.8887-2.5810.45942.8521-0.82565.7134-0.36832.2717-1.2541-1.9762-0.3964-0.00690.0019-1.80770.53212.1019-0.10480.09351.2375-0.33471.024728.0966-15.0681-16.0073
103.484-2.081-1.5182.39081.46143.9636-0.56470.27-0.4832-1.32350.4396-0.14951.2841-0.13260.10650.9927-0.13680.05140.5712-0.07390.663824.9964-14.57832.2596
112.45310.0751.33833.5395-5.32929.1803-0.4504-0.1232-0.3036-0.8928-0.0783-1.41771.26631.48660.14270.97370.10560.34620.7226-0.02521.281634.0506-13.24851.7388
124.73231.6417-1.50965.81114.72849.3621-2.3244-0.2989-1.3413-0.6278-0.7561-1.90391.3594-0.19972.15042.33720.18320.36511.0505-0.021.567732.3341-26.8408-0.5686
134.37541.18961.80643.3272-0.28870.9729-0.1070.68860.2224-0.11070.1719-1.82411.79740.4559-0.27211.74340.19620.63210.793-0.0161.126535.4449-12.9119-8.9787
146.23285.3094-1.02567.095-3.13532.2876-0.6438-0.5962-1.68440.7448-0.57970.6512-1.03680.44461.18981.7229-0.04790.77611.06870.06681.797442.36129.5971-14.5595
155.89046.0777-6.136.3563-6.43596.42770.00041.88760.0114-0.36070.73191.2887-3.09340.3546-1.49521.3203-0.118-0.05090.9399-0.00051.139232.7914.9979-10.7994
167.92125.75412.48444.7319-0.64132.01440.86820.2409-1.42740.27050.69560.29351.1296-2.6004-1.33140.76920.0123-0.18531.1196-0.09931.948922.25439.1159-3.7017
172.1598-0.19770.69145.5125-1.89526.5287-0.3337-0.84161.07080.95820.2745-0.4125-0.47941.27060.2690.810.2427-0.08331.1252-0.40820.597626.6592-3.883126.4263
184.3899-1.05962.24524.1558-0.54944.3622-0.5275-0.45150.4875-0.12230.42020.4838-0.236-0.2512-0.05010.5780.07560.00360.5055-0.02320.615511.141-5.836712.6085
193.92461.09022.50213.6089-1.10732.6629-0.4132-0.32241.1491-0.3750.38241.5623-0.9298-0.68770.01050.69610.2688-0.24870.71850.07391.2472-1.111.43526.2766
202.8264-0.10541.44983.8988-0.09821.9779-0.57671.05730.2343-1.59890.62980.0916-1.1530.2753-0.08061.5299-0.6047-0.18291.27350.29440.63144.4521-12.0647-25.8361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 24:34)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 35:44)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 45:53)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 54:72)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 73:84)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 85:104)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 105:121)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 122:130)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 24:33)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 34:64)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 65:75)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 76:84)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 85:103)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 104:112)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 113:122)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 123:131)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 27:63)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 64:165)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 166:237)
20X-RAY DIFFRACTION20(CHAIN C AND RESID 238:333)

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