[English] 日本語
Yorodumi
- PDB-2z3r: Crystal structure of the IL-15/IL-15Ra complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


NK T cell proliferation / extrathymic T cell selection / positive regulation of protein O-linked glycosylation / natural killer cell proliferation / positive regulation of natural killer cell differentiation / interleukin-15 receptor activity / positive regulation of tissue remodeling / natural killer cell differentiation / cytokine receptor binding / regulation of defense response to virus by host ...NK T cell proliferation / extrathymic T cell selection / positive regulation of protein O-linked glycosylation / natural killer cell proliferation / positive regulation of natural killer cell differentiation / interleukin-15 receptor activity / positive regulation of tissue remodeling / natural killer cell differentiation / cytokine receptor binding / regulation of defense response to virus by host / neutrophil activation / interleukin-15-mediated signaling pathway / tyrosine phosphorylation of STAT protein / Interleukin-15 signaling / negative regulation of cold-induced thermogenesis / positive regulation of natural killer cell proliferation / cytokine receptor activity / 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 phagocytosis / positive regulation of T cell proliferation / cell maturation / positive regulation of tyrosine phosphorylation of STAT protein / response to nutrient levels / positive regulation of cytokine production / cytokine activity / cytoplasmic vesicle membrane / positive regulation of inflammatory response / positive regulation of immune response / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / negative regulation of neuron projection development / 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 / Rubrerythrin, domain 2 - #230 / Interleukin-15/Interleukin-21 family / Interleukin 15 / 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 / Rubrerythrin, domain 2 - #230 / Interleukin-15/Interleukin-21 family / Interleukin 15 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein
Interleukin-15 / 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more