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- PDB-6nmy: A Cytokine-receptor complex -

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Basic information

Entry
Database: PDB / ID: 6nmy
TitleA Cytokine-receptor complex
Components
  • (Cytokine receptor common subunit ...) x 2
  • Interleukin-3
  • Interleukin-3 receptor subunit alpha
KeywordsCYTOKINE / cytokine-receptor complex / receptor assembly / cell surface
Function / homology
Function and homology information


interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway ...interleukin-3 receptor activity / interleukin-3 receptor binding / RUNX1 regulates transcription of genes involved in interleukin signaling / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / cytokine receptor activity / embryonic hemopoiesis / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / Interleukin-3, Interleukin-5 and GM-CSF signaling / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / coreceptor activity / 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 / signaling receptor activity / nervous system development / RAF/MAP kinase cascade / response to lipopolysaccharide / receptor complex / immune response / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / 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 / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Short hematopoietin receptor, family 2, conserved site ...Immunoglobulin-like - #3850 / Interleukin-3 / : / Interleukin-3 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Short hematopoietin receptor family 1 signature. / Type I cytokine receptor, cytokine-binding domain / Interferon-alpha/beta receptor, fibronectin type III / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Growth Hormone; Chain: A; - #10 / Growth Hormone; Chain: A; / Four-helical cytokine-like, core / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-3 / Interleukin-3 receptor subunit alpha / Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.301 Å
AuthorsDhagat, U. / Kan, W.L. / Hercus, T.R. / Broughton, S.E. / Nero, T.L. / Lopez, A.F. / Parker, M.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Cancer Discov / Year: 2023
Title: Distinct Assemblies of Heterodimeric Cytokine Receptors Govern Stemness Programs in Leukemia.
Authors: Kan, W.L. / Dhagat, U. / Kaufmann, K.B. / Hercus, T.R. / Nero, T.L. / Zeng, A.G.X. / Toubia, J. / Barry, E.F. / Broughton, S.E. / Gomez, G.A. / Benard, B.A. / Dottore, M. / Cheung Tung ...Authors: Kan, W.L. / Dhagat, U. / Kaufmann, K.B. / Hercus, T.R. / Nero, T.L. / Zeng, A.G.X. / Toubia, J. / Barry, E.F. / Broughton, S.E. / Gomez, G.A. / Benard, B.A. / Dottore, M. / Cheung Tung Shing, K.S. / Boutzen, H. / Samaraweera, S.E. / Simpson, K.J. / Jin, L. / Goodall, G.J. / Begley, C.G. / Thomas, D. / Ekert, P.G. / Tvorogov, D. / D'Andrea, R.J. / Dick, J.E. / Parker, M.W. / Lopez, A.F.
History
DepositionJan 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: 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_validate_close_contact / 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.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.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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 11, 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
Revision 2.2Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Interleukin-3 receptor subunit alpha
M: Interleukin-3 receptor subunit alpha
A: Cytokine receptor common subunit beta
C: Cytokine receptor common subunit beta
I: Interleukin-3
J: Interleukin-3
B: Cytokine receptor common subunit beta
D: Cytokine receptor common subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,06416
Polymers187,7698
Non-polymers4,2958
Water21612
1
F: Interleukin-3 receptor subunit alpha
A: Cytokine receptor common subunit beta
J: Interleukin-3
B: Cytokine receptor common subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5238
Polymers93,8854
Non-polymers2,6384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: Interleukin-3 receptor subunit alpha
C: Cytokine receptor common subunit beta
I: Interleukin-3
D: Cytokine receptor common subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5418
Polymers93,8854
Non-polymers1,6574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.647, 157.251, 168.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules FMIJ

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


Mass: 33225.520 Da / Num. of mol.: 2 / Mutation: N194Q
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
#3: Protein 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: 13382.270 Da / Num. of mol.: 2 / Mutation: W13Y
Source method: isolated from a genetically manipulated source
Details: The first 4 N-terminal residues (GAMG) are derived from fusion protein
Source: (gene. exp.) Homo sapiens (human) / Gene: IL3 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P08700

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Cytokine receptor common subunit ... , 2 types, 4 molecules ACBD

#2: Protein Cytokine receptor common subunit beta / CDw131 / GM-CSF/IL-3/IL-5 receptor common beta subunit


Mass: 24585.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RB, IL3RB, IL5RB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32927
#4: Protein Cytokine receptor common subunit beta / CDw131 / GM-CSF/IL-3/IL-5 receptor common beta subunit


Mass: 22691.234 Da / Num. of mol.: 2 / Mutation: N346Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2RB, IL3RB, IL5RB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32927

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Sugars , 4 types, 8 molecules

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


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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 natural 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
#8: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural 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, 12 molecules

#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.93 Å3/Da / Density % sol: 68.69 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Crystals were grown in 10 mM Tris pH6.8, 8% PEG 8000, 0.15 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.3→47.76 Å / Num. obs: 45227 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 97.58 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.081 / Rrim(I) all: 0.194 / Net I/σ(I): 8.8 / Num. measured all: 248002 / Scaling rejects: 95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.3-3.425.61.7282448843680.310.8071.9141.199.5
12.78-47.764.60.02738838360.9990.0130.0341.195

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.39 Å47.72 Å
Translation3.39 Å47.72 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.15data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NKQ, 5UV8

4nkq

5uv8


Resolution: 3.301→47.448 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 2233 4.95 %RANDOM
Rwork0.2364 42916 --
obs0.2384 45149 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.51 Å2 / Biso mean: 95.1938 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.301→47.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12678 0 285 12 12975
Biso mean--133.92 76.94 -
Num. residues----1571
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.301-3.37240.40711380.3917264799
3.3724-3.45090.36191490.37142609100
3.4509-3.53710.38151350.3372652100
3.5371-3.63280.34921680.31852614100
3.6328-3.73960.33491440.30672668100
3.7396-3.86030.33491300.29352668100
3.8603-3.99820.32991370.27862656100
3.9982-4.15820.32551310.25472660100
4.1582-4.34730.27851260.23642698100
4.3473-4.57630.23791160.21322693100
4.5763-4.86280.22721300.20532683100
4.8628-5.23780.25551510.19652684100
5.2378-5.76410.25991590.20322679100
5.7641-6.59620.26381560.2242713100
6.5962-8.30330.26191400.21282745100
8.3033-47.4480.21651230.1906284798
Refinement TLS params.Method: refined / Origin x: 21.9225 Å / Origin y: 6.5856 Å / Origin z: 24.6947 Å
111213212223313233
T0.6564 Å20.055 Å20.0642 Å2-0.8364 Å20.0862 Å2--0.6774 Å2
L0.2107 °2-0.0572 °2-0.005 °2-1.0793 °2-0.0536 °2--0.1449 °2
S-0.0495 Å °-0.1211 Å °-0.0638 Å °0.0063 Å °0.0631 Å °0.091 Å °0.0732 Å °0.0384 Å °-0.0108 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allF26 - 411
2X-RAY DIFFRACTION1allM28 - 405
3X-RAY DIFFRACTION1allA25 - 502
4X-RAY DIFFRACTION1allC25 - 401
5X-RAY DIFFRACTION1allI13 - 120
6X-RAY DIFFRACTION1allJ13 - 120
7X-RAY DIFFRACTION1allB241 - 436
8X-RAY DIFFRACTION1allD241 - 437
9X-RAY DIFFRACTION1allE1 - 13

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