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- PDB-2z3r: Crystal structure of the IL-15/IL-15Ra complex -

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Basic information

Entry
Database: PDB / ID: 2z3r
TitleCrystal structure of the IL-15/IL-15Ra complex
Components
  • Interleukin-15
  • Interleukin-15 receptor alpha chain
KeywordsCYTOKINE/CYTOKINE RECEPTOR / Protein-Protein complex / CYTOKINE-CYTOKINE RECEPTOR COMPLEX
Function / homology
Function and homology information


extrathymic T cell selection / positive regulation of protein O-linked glycosylation / NK T cell proliferation / natural killer cell proliferation / positive regulation of natural killer cell differentiation / interleukin-15 receptor activity / positive regulation of tissue remodeling / natural killer cell differentiation / neutrophil activation / cytokine receptor binding ...extrathymic T cell selection / positive regulation of protein O-linked glycosylation / NK T cell proliferation / natural killer cell proliferation / positive regulation of natural killer cell differentiation / interleukin-15 receptor activity / positive regulation of tissue remodeling / natural killer cell differentiation / neutrophil activation / cytokine receptor binding / regulation of defense response to virus by host / tyrosine phosphorylation of STAT protein / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / positive regulation of natural killer cell proliferation / cytokine receptor activity / negative regulation of cold-induced thermogenesis / regulation of T cell differentiation / positive regulation of interleukin-17 production / cell surface receptor signaling pathway via JAK-STAT / macrophage differentiation / lymph node development / positive regulation of T cell proliferation / positive regulation of phagocytosis / positive regulation of tyrosine phosphorylation of STAT protein / cell maturation / response to nutrient levels / positive regulation of cytokine production / cytokine activity / cytoplasmic vesicle membrane / positive regulation of inflammatory response / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / negative regulation of neuron projection development / cell-cell signaling / nuclear membrane / endosome / nuclear speck / immune response / Golgi membrane / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein kinase binding / Golgi apparatus / cell surface / signal transduction / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Interleukin-15 / Interleukin-15, mammal / Interleukin-15 receptor subunit alpha / Interleukin-15/Interleukin-21 / Interleukin-15/Interleukin-21 family / Interleukin 15 / Rubrerythrin, domain 2 - #230 / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. ...Interleukin-15 / Interleukin-15, mammal / Interleukin-15 receptor subunit alpha / Interleukin-15/Interleukin-21 / Interleukin-15/Interleukin-21 family / Interleukin 15 / Rubrerythrin, domain 2 - #230 / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Rubrerythrin, domain 2 / Single Sheet / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-15 / Interleukin-15 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChirifu, M. / Yamagata, Y. / Davis, S.J. / Ikemizu, S.
CitationJournal: Nat.Immunol. / Year: 2007
Title: Crystal structure of the IL-15-IL-15Ralpha complex, a cytokine-receptor unit presented in trans
Authors: Chirifu, M. / Hayashi, C. / Nakamura, T. / Toma, S. / Shuto, T. / Kai, H. / Yamagata, Y. / Davis, S.J. / Ikemizu, S.
History
DepositionJun 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-15
B: Interleukin-15 receptor alpha chain
C: Interleukin-15
D: Interleukin-15 receptor alpha chain
E: Interleukin-15
F: Interleukin-15 receptor alpha chain
G: Interleukin-15
H: Interleukin-15 receptor alpha chain
I: Interleukin-15
J: Interleukin-15 receptor alpha chain
K: Interleukin-15
L: Interleukin-15 receptor alpha chain
M: Interleukin-15
N: Interleukin-15 receptor alpha chain
O: Interleukin-15
P: Interleukin-15 receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,40220
Polymers198,03316
Non-polymers3684
Water9,350519
1
A: Interleukin-15
B: Interleukin-15 receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9384
Polymers24,7542
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Interleukin-15
D: Interleukin-15 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)24,7542
Polymers24,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Interleukin-15
F: Interleukin-15 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)24,7542
Polymers24,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Interleukin-15
H: Interleukin-15 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)24,7542
Polymers24,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Interleukin-15
J: Interleukin-15 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)24,7542
Polymers24,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Interleukin-15
L: Interleukin-15 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)24,7542
Polymers24,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Interleukin-15
N: Interleukin-15 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)24,7542
Polymers24,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Interleukin-15
P: Interleukin-15 receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9384
Polymers24,7542
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.800, 127.035, 191.331
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-15 / IL-15


Mass: 13258.040 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL-15 / Production host: Escherichia coli (E. coli) / References: UniProt: P40933
#2: Protein
Interleukin-15 receptor alpha chain / IL-15R-alpha / IL- 15RA


Mass: 11496.108 Da / Num. of mol.: 8 / Fragment: IL-15Ra, residues in database 31-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL-15RA / Production host: Escherichia coli (E. coli) / References: UniProt: Q13261
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.51 Å3/Da / Density % sol: 50.97 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 119902 / % possible obs: 88.5 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 2→2.06 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.48 / Num. unique all: 10953 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.93 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.723 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24994 2966 2.5 %RANDOM
Rwork0.20499 ---
obs0.20613 116633 100 %-
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: 11.276 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11974 0 24 519 12517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02212229
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.771.95316581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65151513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.05425.524496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.296152231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3581535
X-RAY DIFFRACTIONr_chiral_restr0.1220.21974
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028791
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.25524
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.28551
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2599
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.2214
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1591.57883
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84212505
X-RAY DIFFRACTIONr_scbond_it2.75934908
X-RAY DIFFRACTIONr_scangle_it4.0914.54076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 199 -
Rwork0.25 7890 -
obs--100 %
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)
14.0325-0.87321.97093.40120.22283.17980.30390.204-0.5451-0.15960.15390.1040.0618-0.0987-0.4579-0.09820.0072-0.0035-0.05460.0818-0.0082-1.44828.619627.4445
23.22661.84611.07679.05710.42261.55130.1237-0.2682-0.03210.4511-0.0720.1206-0.0654-0.0626-0.0518-0.07070.02890.0626-0.0550.033-0.085415.42469.902843.7928
32.74081.4188-0.63543.2707-0.19691.95270.07620.05380.28180.03430.00970.3497-0.1119-0.0426-0.0859-0.06370.01280.0405-0.07790.0195-0.06519.604643.682339.5854
44.1084.7427-0.64046.19650.2051.71370.3288-0.30730.27360.3585-0.16790.193-0.0270.0437-0.1609-0.07650.01870.0859-0.02920.0082-0.05632.019632.582950.8141
52.45370.21971.87982.04910.48973.09710.1408-0.0006-0.2748-0.07250.14630.04950.1778-0.0853-0.2871-0.0374-0.0016-0.0279-0.03420.0434-0.0925-2.437510.408175.6199
62.3181.60570.58367.68690.14221.20650.1097-0.2516-0.04620.3742-0.0725-0.0332-0.04550.0002-0.0372-0.06160.01650.015-0.02160.0137-0.123415.175711.812692.0728
74.24110.6404-0.54123.0432-0.22091.49380.11550.18080.50740.0096-0.04970.2846-0.03680.0089-0.0658-0.08120.02580.0247-0.06990.0198-0.095519.703345.741588.5822
83.19623.2197-0.31214.39890.06551.26050.233-0.28330.2950.1981-0.12770.049-0.01110.0473-0.1053-0.05540.00030.0345-0.0175-0.0431-0.10221.793634.471599.4674
93.7636-0.04291.0343.58550.03591.65860.1349-0.1506-0.27740.0176-0.08130.03510.04040.0335-0.0537-0.0732-0.01480.025-0.05270.0071-0.173260.533515.968554.5121
102.9722-3.2417-0.36947.14721.4351.90440.04780.2385-0.0841-0.3785-0.03820.1911-0.05850.0832-0.0096-0.0471-0.0175-0.019-0.0135-0.0139-0.1642.905127.154943.3686
112.0674-0.1374-1.53121.41760.00962.79150.0683-0.01610.05910.07550.12750.0529-0.1159-0.0523-0.1958-0.0529-0.00580.0092-0.02660.0669-0.128138.81750.801967.4853
123.4546-2.7332-1.12588.38240.55561.14850.10440.2078-0.0698-0.4144-0.0809-0.23690.0334-0.0665-0.0235-0.0549-0.0320.0252-0.04870.0151-0.134256.217649.763251.1866
134.4338-1.86571.08252.75470.05251.99790.1968-0.1008-0.7275-0.04440.00760.42740.06520.0376-0.2044-0.088-0.0145-0.0381-0.10750.00970.049160.812117.87867.4607
144.28-2.68950.17866.4382.18892.01840.17850.2864-0.3217-0.3365-0.0810.2473-0.07490.0798-0.0975-0.0619-0.0033-0.048-0.0498-0.0512-0.085543.264229.0381-3.8761
153.35020.2939-1.61632.88370.22423.22020.1462-0.08670.14190.11870.10170.0206-0.0477-0.0666-0.2478-0.0468-0.01810.007-0.03820.0793-0.105438.841453.128519.7359
163.7426-2.2467-0.9247.91530.52720.79810.07450.2503-0.099-0.3672-0.0538-0.02070.0545-0.0353-0.0207-0.0412-0.0232-0.0044-0.05270.0177-0.12156.490551.69783.6486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1126 - 117
2X-RAY DIFFRACTION2BB1 - 706 - 75
3X-RAY DIFFRACTION3CC1 - 1146 - 119
4X-RAY DIFFRACTION4DD1 - 706 - 75
5X-RAY DIFFRACTION5EE1 - 1146 - 119
6X-RAY DIFFRACTION6FF1 - 706 - 75
7X-RAY DIFFRACTION7GG1 - 1146 - 119
8X-RAY DIFFRACTION8HH1 - 706 - 75
9X-RAY DIFFRACTION9II1 - 1146 - 119
10X-RAY DIFFRACTION10JJ1 - 706 - 75
11X-RAY DIFFRACTION11KK1 - 1146 - 119
12X-RAY DIFFRACTION12LL1 - 706 - 75
13X-RAY DIFFRACTION13MM1 - 1146 - 119
14X-RAY DIFFRACTION14NN1 - 706 - 75
15X-RAY DIFFRACTION15OO1 - 1136 - 118
16X-RAY DIFFRACTION16PP1 - 706 - 75

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