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- PDB-2b5i: cytokine receptor complex -

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Basic information

Entry
Database: PDB / ID: 2b5i
Titlecytokine receptor complex
Components
  • (Interleukin-2 receptor ...IL-2 receptor) x 2
  • Cytokine receptor common gamma chain
  • Interleukin-2Interleukin 2
KeywordsCYTOKINE/CYTOKINE RECEPTOR / four-helix bundle / Fibronectin domain / CYTOKINE-CYTOKINE RECEPTOR COMPLEX
Function / homology
Function and homology information


regulation of T cell tolerance induction / interleukin-7-mediated signaling pathway / mature B cell differentiation / interleukin-2 receptor complex / interleukin-2 receptor activity / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation ...regulation of T cell tolerance induction / interleukin-7-mediated signaling pathway / mature B cell differentiation / interleukin-2 receptor complex / interleukin-2 receptor activity / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / activation-induced cell death of T cells / positive regulation of tissue remodeling / positive regulation of T cell differentiation in thymus / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / Interleukin-9 signaling / Interleukin-21 signaling / leukocyte activation involved in immune response / interleukin-9-mediated signaling pathway / positive regulation of isotype switching to IgG isotypes / interleukin-4-mediated signaling pathway / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-2-mediated signaling pathway / natural killer cell activation / STAT3 nuclear events downstream of ALK signaling / activated T cell proliferation / positive regulation of regulatory T cell differentiation / protein kinase C-activating G protein-coupled receptor signaling pathway / interleukin-15-mediated signaling pathway / kinase activator activity / inflammatory response to antigenic stimulus / negative regulation of B cell apoptotic process / Interleukin-15 signaling / cytokine receptor activity / Interleukin-2 signaling / positive regulation of dendritic spine development / positive regulation of T cell differentiation / positive regulation of B cell differentiation / cytokine binding / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / immunoglobulin mediated immune response / positive regulation of immunoglobulin production / T cell differentiation / Interleukin receptor SHC signaling / coreceptor activity / positive regulation of phagocytosis / positive regulation of B cell proliferation / Notch signaling pathway / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / Interleukin-7 signaling / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of inflammatory response / cytokine-mediated signaling pathway / positive regulation of type II interferon production / cell-cell signaling / gene expression / T cell differentiation in thymus / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / protein-containing complex assembly / response to ethanol / Interleukin-4 and Interleukin-13 signaling / transcription by RNA polymerase II / adaptive immune response / cell surface receptor signaling pathway / receptor complex / cell adhesion / endosome / immune response / inflammatory response / external side of plasma membrane / apoptotic process / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / cell surface / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / Rubrerythrin, domain 2 - #230 / Interleukin-2 receptor alpha / : / : / Cytokine receptor-like factor 2-like, D1 domain / Cytokine receptor-like factor 2-like, D2 domain / Interleukin-2 / Interleukin-2, conserved site ...Interleukin-2 receptor subunit beta, N-terminal / Interleukin-2 receptor subunit beta N-terminal domain 1 / Rubrerythrin, domain 2 - #230 / Interleukin-2 receptor alpha / : / : / Cytokine receptor-like factor 2-like, D1 domain / Cytokine receptor-like factor 2-like, D2 domain / Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Short hematopoietin receptor family 1 signature. / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Complement Module, domain 1 / Complement Module; domain 1 / Growth Hormone; Chain: A; - #10 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Rubrerythrin, domain 2 / Single Sheet / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-2 receptor subunit alpha / Interleukin-2 receptor subunit beta / Cytokine receptor common subunit gamma / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, X. / Rickert, M. / Garcia, K.C.
CitationJournal: Science / Year: 2005
Title: Structure of the quaternary complex of interleukin-2 with its alpha, beta, and gammac receptors.
Authors: Wang, X. / Rickert, M. / Garcia, K.C.
History
DepositionSep 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-2
B: Interleukin-2 receptor beta chain
C: Cytokine receptor common gamma chain
D: Interleukin-2 receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9748
Polymers88,6834
Non-polymers1,2914
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.913, 87.709, 130.177
Angle α, β, γ (deg.)90.00, 116.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Interleukin-2 / Interleukin 2 / IL-2 / T-cell growth factor / TCGF / Aldesleukin


Mass: 15435.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60568
#3: Protein Cytokine receptor common gamma chain / Gamma-C / Interleukin-2 receptor gamma chain / IL-2R gamma chain / P64 / CD132 antigen


Mass: 23912.684 Da / Num. of mol.: 1 / Mutation: N53Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RG / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P31785

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Interleukin-2 receptor ... , 2 types, 2 molecules BD

#2: Protein Interleukin-2 receptor beta chain / IL-2 receptor / P70-75 / High affinity IL-2 receptor beta subunit / CD122 antigen


Mass: 24761.123 Da / Num. of mol.: 1 / Mutation: N3Q,N17Q,N45Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14784
#4: Protein Interleukin-2 receptor alpha chain / IL-2 receptor alpha subunit / IL-2-RA / IL2-RA / p55 / TAC antigen / CD25 antigen


Mass: 24573.492 Da / Num. of mol.: 1 / Mutation: N68Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01589

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Sugars , 2 types, 4 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 171 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.2 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 29% Pentaerythritol Ethoxylate 15/4; 50 mM Ammonium Sulfate; 50 mM Bis Tris, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Jan 21, 2003
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 58395 / Num. obs: 57577 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.26 Å / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.914 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.238 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26883 2560 5 %RANDOM
Rwork0.22303 ---
all0.22535 48601 --
obs0.22535 48305 99.39 %-
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: 57.657 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å2-1.29 Å2
2--3.33 Å20 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 84 171 5463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215454
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9417418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.645620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80123.858267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96115928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1121536
X-RAY DIFFRACTIONr_chiral_restr0.090.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024101
X-RAY DIFFRACTIONr_nbd_refined0.2040.22265
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23567
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.25
X-RAY DIFFRACTIONr_mcbond_it0.5171.53260
X-RAY DIFFRACTIONr_mcangle_it0.87925144
X-RAY DIFFRACTIONr_scbond_it1.34132548
X-RAY DIFFRACTIONr_scangle_it2.1374.52274
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 176 -
Rwork0.32 3483 -
obs--97.5 %
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)
16.4618-0.12510.43367.39681.84285.63420.0801-0.1984-0.11980.24210.0656-0.72880.11170.4081-0.1457-0.2408-0.18570.011-0.12850.0108-0.23078.2051-24.283328.5622
27.61874.89762.08585.25271.72052.43970.1364-0.74520.65940.3179-0.36750.2807-0.0523-0.19690.2311-0.1917-0.07130.031-0.1575-0.0914-0.1777-7.4153-15.092148.0441
33.07730.5879-2.31430.7145-0.84134.277-0.09620.2125-0.4018-0.2901-0.01720.03320.5479-0.31030.1135-0.0746-0.1664-0.0361-0.25660.0148-0.2441-16.5754-40.633720.7271
45.073-5.05845.95345.8501-6.18757.3265-0.06620.58120.2585-0.14190.1583-0.19380.10790.1931-0.09210.0793-0.06750.03010.2254-0.15520.503633.8088-36.935436.7921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1336 - 133
2X-RAY DIFFRACTION2CC34 - 2241 - 191
3X-RAY DIFFRACTION3BB6 - 2076 - 207
4X-RAY DIFFRACTION4DD1 - 1651 - 165

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