[English] 日本語
Yorodumi
- PDB-2psm: Crystal structure of Interleukin 15 in complex with Interleukin 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2psm
TitleCrystal structure of Interleukin 15 in complex with Interleukin 15 receptor alpha
Components
  • Interleukin-15 receptor alpha chain
  • Interleukin-15Interleukin 15
KeywordsCYTOKINE / Glycoprotein / Secreted / Alternative splicing / Endoplasmic reticulum / Golgi apparatus / Membrane / Nucleus / Phosphorylation / Receptor / Sushi / Transmembrane / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


NK T cell proliferation / extrathymic T cell selection / positive regulation of protein O-linked glycosylation / hyaluronan metabolic process / Interleukin-15 signaling / positive regulation of natural killer cell differentiation / interleukin-15 receptor activity / skeletal muscle atrophy / : / neutrophil activation ...NK T cell proliferation / extrathymic T cell selection / positive regulation of protein O-linked glycosylation / hyaluronan metabolic process / Interleukin-15 signaling / positive regulation of natural killer cell differentiation / interleukin-15 receptor activity / skeletal muscle atrophy / : / neutrophil activation / cytokine receptor binding / cellular response to vitamin D / regulation of defense response to virus by host / interleukin-15-mediated signaling pathway / tyrosine phosphorylation of STAT protein / negative regulation of cold-induced thermogenesis / regulation of T cell differentiation / positive regulation of natural killer cell proliferation / 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 / cytokine activity / positive regulation of cytokine production / negative regulation of smooth muscle cell proliferation / positive regulation of immune response / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of neuron projection development / cytoplasmic vesicle / nuclear membrane / membrane => GO:0016020 / nuclear speck / immune response / inflammatory response / positive regulation of cell population proliferation / protein kinase binding / cell surface / 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 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) ...: / 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 / Sushi repeat (SCR repeat) / 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
BENZAMIDINE / Interleukin-15 / Interleukin-15 receptor subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsOlsen, S.K. / Murayama, K. / Kishishita, S. / Kukimoto-Niino, M. / Terada, T. / Shirouzu, M. / Ota, N. / Kanagawa, O. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of the Interleukin-15{middle dot}Interleukin-15 Receptor {alpha} Complex: INSIGHTS INTO TRANS AND CIS PRESENTATION
Authors: Olsen, S.K. / Ota, N. / Kishishita, S. / Kukimoto-Niino, M. / Murayama, K. / Uchiyama, H. / Toyama, M. / Terada, T. / Shirouzu, M. / Kanagawa, O. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION ...BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. DETAILS: AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-15
F: Interleukin-15 receptor alpha chain
B: Interleukin-15
C: Interleukin-15 receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4405
Polymers44,3204
Non-polymers1201
Water1,63991
1
A: Interleukin-15
F: Interleukin-15 receptor alpha chain


Theoretical massNumber of molelcules
Total (without water)22,1602
Polymers22,1602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
MethodPISA
2
B: Interleukin-15
C: Interleukin-15 receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2803
Polymers22,1602
Non-polymers1201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.450, 118.450, 76.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

-
Components

#1: Protein Interleukin-15 / Interleukin 15 / IL-15


Mass: 13781.437 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell Free Expression: E.coli / Gene: Il15 / Production host: Cell free synthesis / References: UniProt: P48346
#2: Protein Interleukin-15 receptor alpha chain / IL-15R-alpha / IL- 15RA


Mass: 8378.438 Da / Num. of mol.: 2 / Fragment: UNP residues 33-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell Free Expression: E.coli / Gene: Il15ra / Production host: Cell free synthesis / References: UniProt: Q60819
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.7M Na/K Phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 10, 2007
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 53064 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Rsym value: 0.057 / Net I/σ(I): 23
Reflection shellResolution: 2.19→2.27 Å / Mean I/σ(I) obs: 18.6 / Num. unique all: 2777 / Rsym value: 0.163 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.19→25 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1418 -random
Rwork0.224 ---
all-28390 --
obs-53064 99.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.2 Å2--
2---3.2 Å2-
3---6.4 Å2
Refinement stepCycle: LAST / Resolution: 2.19→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 9 91 2942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

+
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