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- EMDB-41369: IL-3 Receptor Complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41369
TitleIL-3 Receptor Complex
Map data
Sample
  • Complex: IL-3 Receptor Complex
    • Protein or peptide: IL-3 Receptor Alpha
    • Protein or peptide: Common Beta Receptor
    • Protein or peptide: IL-3
KeywordsIL-3 / cytokine / receptor / SIGNALING PROTEIN
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 / embryonic hemopoiesis / cytokine receptor activity / 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 / nervous system development / signaling receptor activity / 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
Interleukin-3 / Interleukin-3 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / : / 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. ...Interleukin-3 / Interleukin-3 / IL-3 receptor alpha chain, N-terminal / IL-3 receptor alpha chain N-terminal domain / : / 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-3 / Interleukin-3 receptor subunit alpha / Cytokine receptor common subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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_41369.png

Downloads & links

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Map

FileDownload / File: emd_41369.map.gz / Format: CCP4 / Size: 25.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.26271 Å
Density
Contour LevelBy AUTHOR: 0.139
Minimum - Maximum-0.11238886 - 2.0312564
Average (Standard dev.)0.00081038347 (±0.024176195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions188188188
Spacing188188188
CellA=B=C: 237.38881 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41369_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41369_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41369_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-3 Receptor Complex

EntireName: IL-3 Receptor Complex
Components
  • Complex: IL-3 Receptor Complex
    • Protein or peptide: IL-3 Receptor Alpha
    • Protein or peptide: Common Beta Receptor
    • Protein or peptide: IL-3

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Supramolecule #1: IL-3 Receptor Complex

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

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Macromolecule #1: IL-3 Receptor Alpha

MacromoleculeName: IL-3 Receptor Alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: DYKDDDDKKE DPNPPITNLR MKAKAQQLTW DLNRNVTDIE CVKDADYSMP AVNNSYCQFG AISLCEVTNY TVRVANPPFS TWILFPENSG KPWAGAENLT CWIHDVDFLS CSWAVGPGAP ADVQYDLYLN VANRRQQYEC LHYKTDAQGT RIGCRFDDIS RLSSGSQSSH ...String:
DYKDDDDKKE DPNPPITNLR MKAKAQQLTW DLNRNVTDIE CVKDADYSMP AVNNSYCQFG AISLCEVTNY TVRVANPPFS TWILFPENSG KPWAGAENLT CWIHDVDFLS CSWAVGPGAP ADVQYDLYLN VANRRQQYEC LHYKTDAQGT RIGCRFDDIS RLSSGSQSSH ILVRGRSAAF GIPCTDKFVV FSQIEILTPP NMTAKCNKTH SFMHWKMRSH FNRKFRYELQ IQKRMQPVIT EQVRDRTSFQ LLNPGTYTVQ IRARERVYEF LSAWSTPQRF ECDQEEGANT RAWRTSGGGG STTAPSAQLK KKLQALKKKN AQLKWKLQAL KKKLAQGAAE DQVDPRLIDG KHHHHHHHH

UniProtKB: Interleukin-3 receptor subunit alpha

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Macromolecule #2: Common Beta Receptor

MacromoleculeName: Common Beta Receptor / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: DYKDDDDKMV SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKQH DFFKSAMPEG YVQERTIFFK DDGNYKTRAE VKFEGDTLVN RIELKGIDFK EDGNILGHKL EYNYNSHNVY IMADKQKNGI ...String:
DYKDDDDKMV SKGEELFTGV VPILVELDGD VNGHKFSVSG EGEGDATYGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKQH DFFKSAMPEG YVQERTIFFK DDGNYKTRAE VKFEGDTLVN RIELKGIDFK EDGNILGHKL EYNYNSHNVY IMADKQKNGI KVNFKIRHNI EDGSVQLADH YQQNTPIGDG PVLLPDNHYL STQSALSKDP NEKRDHMVLL EFVTAAGITL GMDELYKLEV LFQGPGSGAE ETIPLQTLRC YNDYTSHITC RWADTQDAQR LVNVTLIRRV NEDLLEPVSC DLSDDMPWSA CPHPRCVPRR CVIPCQSFVV TDVDYFSFQP DRPLGTRLTV TLTQHVQPPE PRDLQISTDQ DHFLLTWSVA LGSPQSHWLS PGDLEFEVVY KRLQDSWEDA AILLSNTSQA TLGPEHLMPS STYVARVRTR LAPGSRLSGR PSKWSPEVCW DSQPGDEAQP QNLECFFDGA AVLSCSWEVR KEVASSVSFG LFYKPSPDAG EEECSPVLRE GLGSLHTRHH CQIPVPDPAT HGQYIVSVQP RRAEKHIKSS VNIQMAPPSL NVTKDGDSYS LRWETMKMRY EHIDHTFEIQ YRKDTATWKD SKTETLQNAH SMALPALEPS TRYWARVRVR TSRTGYNGIW SEWSEARSWD TESVLPMGGG GSTTAPSAQL EKELQALEKE NAQLEWELQA LEKELAQ

UniProtKB: Cytokine receptor common subunit beta

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Macromolecule #3: IL-3

MacromoleculeName: IL-3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString:
DYKDDDDKAP MTQTTPLKTS WVNCSNMIDE IITHLKQPPL PLLDFNNLNG EDQDILMENN LRRPNLEAFN RAVKSLQNAS AIESILKNLL PCLPLATAAP TRHPIHIKDG DWNEFRRKLT FYLKTLENAQ AQQTTLSLAI FGAAEDQVDP RLIDGKHHHH HHHH

UniProtKB: Interleukin-3

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.8 e/Å2
Electron beamAcceleration voltage: 200 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

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 514634
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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