+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41367 | |||||||||
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Title | Structure of the IL-5 Signaling Complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | IL-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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Caveney NA / Garcia KC | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41367.map.gz | 18.2 MB | EMDB map data format | |
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Header (meta data) | emd-41367-v30.xml emd-41367.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41367_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_41367.png | 49.2 KB | ||
Masks | emd_41367_msk_1.map | 20.8 MB | Mask map | |
Filedesc metadata | emd-41367.cif.gz | 6 KB | ||
Others | emd_41367_half_map_1.map.gz emd_41367_half_map_2.map.gz | 19.3 MB 19.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41367 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41367 | HTTPS FTP |
-Validation report
Summary document | emd_41367_validation.pdf.gz | 685.4 KB | Display | EMDB validaton report |
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Full document | emd_41367_full_validation.pdf.gz | 685 KB | Display | |
Data in XML | emd_41367_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | emd_41367_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41367 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41367 | HTTPS FTP |
-Related structure data
Related structure data | 8tldMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41367.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.306 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41367_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41367_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41367_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : IL-5 Receptor Complex
Entire | Name: IL-5 Receptor Complex |
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Components |
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-Supramolecule #1: IL-5 Receptor Complex
Supramolecule | Name: IL-5 Receptor Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Cytokine receptor common subunit beta
Macromolecule | Name: Cytokine receptor common subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 81.07875 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Interleukin-5
Macromolecule | Name: Interleukin-5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.836051 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DYKDDDDKIP TEIPTSALVK ETLALLSTHR TLLIANETLR IPVPVHKNHQ LCTEEIFQGI GTLESQTVQG GTVERLFKNL SLIKKYIDG QKKKCGEERR RVNQFLDYLQ EFLGVMNTEW IIESGAAEDQ VDPRLIDGKH HHHHHHH UniProtKB: Interleukin-5 |
-Macromolecule #3: Interleukin-5 receptor subunit alpha
Macromolecule | Name: Interleukin-5 receptor subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.590176 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |