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- PDB-2psm: Crystal structure of Interleukin 15 in complex with Interleukin 1... -

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Basic information

Entry
Database: PDB / ID: 2psm
TitleCrystal structure of Interleukin 15 in complex with Interleukin 15 receptor alpha
Components
  • Interleukin-15
  • Interleukin-15 receptor alpha chain
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


extrathymic T cell selection / positive regulation of protein O-linked glycosylation / NK T cell proliferation / hyaluronan metabolic process / natural killer cell proliferation / Interleukin-15 signaling / positive regulation of natural killer cell differentiation / interleukin-15 receptor activity / natural killer cell differentiation / neutrophil activation ...extrathymic T cell selection / positive regulation of protein O-linked glycosylation / NK T cell proliferation / hyaluronan metabolic process / natural killer cell proliferation / Interleukin-15 signaling / positive regulation of natural killer cell differentiation / interleukin-15 receptor activity / natural killer cell differentiation / neutrophil activation / cytokine receptor binding / regulation of defense response to virus by host / interleukin-15-mediated signaling pathway / positive regulation of natural killer cell proliferation / 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 / negative regulation of smooth muscle cell proliferation / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / negative regulation of neuron projection development / cytoplasmic vesicle / nuclear membrane / nuclear speck / immune response / positive regulation of cell population proliferation / protein kinase binding / cell surface / extracellular space / extracellular region / 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 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain ...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 / 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
Revision 2.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

#1: Protein 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


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


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 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

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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

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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

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