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- EMDB-41367: Structure of the IL-5 Signaling Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-41367
TitleStructure of the IL-5 Signaling Complex
Map data
Sample
  • Complex: IL-5 Receptor Complex
    • Protein or peptide: Cytokine receptor common subunit beta
    • Protein or peptide: Interleukin-5
    • Protein or peptide: Interleukin-5 receptor subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIL-5 / cytokine / receptor / SIGNALING PROTEIN
Function / homology
Function and homology information


interleukin-5 receptor activity / regulation of interleukin-5 production / positive regulation of eosinophil differentiation / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / interleukin-5 receptor binding / respiratory gaseous exchange by respiratory system / Surfactant metabolism / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway ...interleukin-5 receptor activity / regulation of interleukin-5 production / positive regulation of eosinophil differentiation / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / interleukin-5 receptor binding / 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 / inflammatory response to antigenic stimulus / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / positive regulation of podosome assembly / cytokine receptor activity / positive regulation of immunoglobulin production / 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 B cell proliferation / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / signaling receptor activity / RAF/MAP kinase cascade / response to lipopolysaccharide / receptor complex / inflammatory response / immune response / external side of plasma membrane / positive regulation of DNA-templated transcription / signal transduction / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Interleukin-5 / Interleukin 5 / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / 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 / Interleukin-6 receptor alpha chain, binding ...Interleukin-5 / Interleukin 5 / : / GM-CSF/IL-3/IL-5 receptor common beta subunit, N-terminal / Cytokine IL-3/IL-5/GM-CSF receptor common beta chain / 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 / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Four-helical cytokine-like, core / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-5 / Cytokine receptor common subunit beta / Interleukin-5 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsCaveney NA / Garcia KC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Organizing structural principles of common beta family signaling
Authors: Caveney NA / Rodriguez GE / Pollmann C / Householder KD / Saxton RA / Piehler J / Garcia KC
History
DepositionJul 26, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41367.png

Downloads & links

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Map

FileDownload / File: emd_41367.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.306 Å
Density
Contour LevelBy AUTHOR: 0.126
Minimum - Maximum-0.023213824 - 2.277234
Average (Standard dev.)0.0013444866 (±0.026384734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 229.856 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41367_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41367_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41367_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : IL-5 Receptor Complex

EntireName: IL-5 Receptor Complex
Components
  • Complex: IL-5 Receptor Complex
    • Protein or peptide: Cytokine receptor common subunit beta
    • Protein or peptide: Interleukin-5
    • Protein or peptide: Interleukin-5 receptor subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: IL-5 Receptor Complex

SupramoleculeName: IL-5 Receptor Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cytokine receptor common subunit beta

MacromoleculeName: Cytokine receptor common subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.07875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKMV SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKQ HDFFKSAMPE GYVQERTIFF KDDGNYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK LEYNYNSHNV Y IMADKQKN ...String:
DYKDDDDKMV SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKQ HDFFKSAMPE GYVQERTIFF KDDGNYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK LEYNYNSHNV Y IMADKQKN GIKVNFKIRH NIEDGSVQLA DHYQQNTPIG DGPVLLPDNH YLSTQSALSK DPNEKRDHMV LLEFVTAAGI TL GMDELYK LEVLFQGPGS GAEETIPLQT LRCYNDYTSH ITCRWADTQD AQRLVNVTLI RRVNEDLLEP VSCDLSDDMP WSA CPHPRC VPRRCVIPCQ SFVVTDVDYF SFQPDRPLGT RLTVTLTQHV QPPEPRDLQI STDQDHFLLT WSVALGSPQS HWLS PGDLE FEVVYKRLQD SWEDAAILLS NTSQATLGPE HLMPSSTYVA RVRTRLAPGS RLSGRPSKWS PEVCWDSQPG DEAQP QNLE CFFDGAAVLS CSWEVRKEVA SSVSFGLFYK PSPDAGEEEC SPVLREGLGS LHTRHHCQIP VPDPATHGQY IVSVQP RRA EKHIKSSVNI QMAPPSLNVT KDGDSYSLRW ETMKMRYEHI DHTFEIQYRK DTATWKDSKT ETLQNAHSMA LPALEPS TR YWARVRVRTS RTGYNGIWSE WSEARSWDTE SVLPMGGGGS TTAPSAQLEK ELQALEKENA QLEWELQALE KELAQ

UniProtKB: Cytokine receptor common subunit beta

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Macromolecule #2: Interleukin-5

MacromoleculeName: Interleukin-5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.836051 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DYKDDDDKIP TEIPTSALVK ETLALLSTHR TLLIANETLR IPVPVHKNHQ LCTEEIFQGI GTLESQTVQG GTVERLFKNL SLIKKYIDG QKKKCGEERR RVNQFLDYLQ EFLGVMNTEW IIESGAAEDQ VDPRLIDGKH HHHHHHH

UniProtKB: Interleukin-5

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Macromolecule #3: Interleukin-5 receptor subunit alpha

MacromoleculeName: Interleukin-5 receptor subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.590176 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKDL LPDEKISLLP PVNFTIKVTG LAQVLLQWKP NPDQEQRNVN LEYQVKINAP KEDDYETRIT ESKCVTILHK GFSASVRTI LQNDHSLLAS SWASAELHAP PGSPGTSIVN LTCTTNTTED NYSRLRSYQV SLHCTWLVGT DAPEDTQYFL Y YRYGSWTE ...String:
DYKDDDDKDL LPDEKISLLP PVNFTIKVTG LAQVLLQWKP NPDQEQRNVN LEYQVKINAP KEDDYETRIT ESKCVTILHK GFSASVRTI LQNDHSLLAS SWASAELHAP PGSPGTSIVN LTCTTNTTED NYSRLRSYQV SLHCTWLVGT DAPEDTQYFL Y YRYGSWTE ECQEYSKDTL GRNIACWFPR TFILSKGRDW LAVLVNGSSK HSAIRPFDQL FALHAIDQIN PPLNVTAEIE GT RLSIQWE KPVSAFPIHC FDYEVKIHNT RNGYLQIEKL MTNAFISIID DLSKYDVQVR AAVSSMCREA GLWSEWSQPI YVG NDEHKP LREGGGGSTT APSAQLKKKL QALKKKNAQL KWKLQALKKK LAQGAAEDQV DPRLIDGKHH HHHHHH

UniProtKB: Interleukin-5 receptor subunit alpha

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 418819
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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