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- PDB-5uwc: Cytokine-receptor complex -

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Basic information

Entry
Database: PDB / ID: 5uwc
TitleCytokine-receptor complex
Components
  • Interleukin-3 receptor subunit alpha
  • Interleukin-3Interleukin 3
KeywordsSIGNALING PROTEIN / Cytokine / Receptor / Signalling
Function / homology
Function and homology information


interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / interleukin-3-mediated signaling pathway / cytokine receptor activity / embryonic hemopoiesis / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / positive regulation of tyrosine phosphorylation of STAT protein ...interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / interleukin-3-mediated signaling pathway / cytokine receptor activity / embryonic hemopoiesis / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / nervous system development / RAF/MAP kinase cascade / receptor complex / immune response / external side of plasma membrane / positive regulation of cell population proliferation / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3850 / Interleukin-3 / Interleukin-3 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Growth Hormone; Chain: A; - #10 ...Immunoglobulin-like - #3850 / Interleukin-3 / Interleukin-3 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Chem-EDT / IMIDAZOLE / Interleukin-3 / Interleukin-3 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBroughton, S.E. / Parker, M.W.
CitationJournal: Nat Commun / Year: 2018
Title: A dual role for the N-terminal domain of the IL-3 receptor in cell signalling.
Authors: Broughton, S.E. / Hercus, T.R. / Nero, T.L. / Kan, W.L. / Barry, E.F. / Dottore, M. / Cheung Tung Shing, K.S. / Morton, C.J. / Dhagat, U. / Hardy, M.P. / Wilson, N.J. / Downton, M.T. / ...Authors: Broughton, S.E. / Hercus, T.R. / Nero, T.L. / Kan, W.L. / Barry, E.F. / Dottore, M. / Cheung Tung Shing, K.S. / Morton, C.J. / Dhagat, U. / Hardy, M.P. / Wilson, N.J. / Downton, M.T. / Schieber, C. / Hughes, T.P. / Lopez, A.F. / Parker, M.W.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Interleukin-3 receptor subunit alpha
I: Interleukin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7618
Polymers47,2242
Non-polymers1,5376
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint5 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.461, 106.461, 96.116
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 2 types, 2 molecules GI

#1: Protein Interleukin-3 receptor subunit alpha / / IL-3RA


Mass: 33253.570 Da / Num. of mol.: 1 / Fragment: UNP residues 20-307 / Mutation: N212Q, A298V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL3RA, IL3R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P26951
#2: Protein Interleukin-3 / Interleukin 3 / IL-3 / Hematopoietic growth factor / Mast cell growth factor / MCGF / Multipotential colony- ...IL-3 / Hematopoietic growth factor / Mast cell growth factor / MCGF / Multipotential colony-stimulating factor / P-cell-stimulating factor


Mass: 13969.933 Da / Num. of mol.: 1 / Fragment: UNP residues 31-152 / Mutation: W32Y, K116W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL3 / Production host: Escherichia coli (E. coli) / References: UniProt: P08700

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#4: 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.: 1
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 , 4 types, 68 molecules

#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID / Ethylenediaminetetraacetic acid


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.33 Å3/Da / Density % sol: 63.06 % / Description: Tetragonal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 20% PEG 8000, 200 mM NaCl and 100 mM citrate-phosphate buffer pH 4.8
PH range: 4.6-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.4→92.2 Å / Num. obs: 23081 / % possible obs: 99 % / Redundancy: 16.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.7
Reflection shellResolution: 2.39→2.4 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZJ, 1JLI

4jzj

1jli


Resolution: 2.4→92.2 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 16.867 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24199 1242 5.1 %RANDOM
Rwork0.21633 ---
obs0.21763 23081 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----1.57 Å2
Refinement stepCycle: 1 / Resolution: 2.4→92.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 103 64 3125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193126
X-RAY DIFFRACTIONr_bond_other_d0.0030.022905
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9654241
X-RAY DIFFRACTIONr_angle_other_deg0.99536669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56923.66153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52215515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4141525
X-RAY DIFFRACTIONr_chiral_restr0.1030.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02763
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7365.7271460
X-RAY DIFFRACTIONr_mcbond_other1.7375.7241459
X-RAY DIFFRACTIONr_mcangle_it3.1158.571818
X-RAY DIFFRACTIONr_mcangle_other3.1148.5741819
X-RAY DIFFRACTIONr_scbond_it1.6326.0131666
X-RAY DIFFRACTIONr_scbond_other1.6316.0141664
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8878.9412423
X-RAY DIFFRACTIONr_long_range_B_refined5.85444.8713295
X-RAY DIFFRACTIONr_long_range_B_other5.85344.8743296
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.396→2.458 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 84 -
Rwork0.285 1650 -
obs--96.6 %
Refinement TLS params.Method: refined / Origin x: 87.4046 Å / Origin y: 55.1976 Å / Origin z: 6.4162 Å
111213212223313233
T0.0294 Å20.0191 Å20.0035 Å2-0.0794 Å20.0295 Å2--0.0231 Å2
L0.9228 °20.8075 °20.2993 °2-1.1998 °20.6958 °2--1.1252 °2
S0.0832 Å °-0.0288 Å °-0.1037 Å °0.0382 Å °-0.0828 Å °-0.1335 Å °0.0844 Å °0.1376 Å °-0.0004 Å °

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