+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14427 | |||||||||
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Title | IL-27 signalling complex | |||||||||
Map data | CryoEM map of the IL-27 signalling complex. | |||||||||
Sample |
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Function / homology | Function and homology information interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / negative regulation of T cell extravasation / negative regulation of cellular extravasation / oncostatin-M receptor activity / negative regulation of T-helper 17 type immune response / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity ...interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / negative regulation of T cell extravasation / negative regulation of cellular extravasation / oncostatin-M receptor activity / negative regulation of T-helper 17 type immune response / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / Interleukin-27 signaling / Interleukin-6 signaling / triglyceride mobilization / interleukin-6 receptor activity / interleukin-6 binding / interleukin-27 receptor activity / Interleukin-35 Signalling / negative regulation of type 2 immune response / oncostatin-M receptor complex / regulation of isotype switching to IgG isotypes / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / interleukin-6 receptor complex / response to Gram-positive bacterium / regulation of Notch signaling pathway / interleukin-6 receptor binding / interleukin-11-mediated signaling pathway / positive regulation of T-helper 1 type immune response / positive regulation of astrocyte differentiation / intestinal epithelial cell development / negative regulation of interleukin-17 production / cytokine receptor activity / positive regulation of Notch signaling pathway / glycogen metabolic process / interleukin-6-mediated signaling pathway / regulation of T cell proliferation / cytokine binding / protein tyrosine kinase activator activity / negative regulation of cytosolic calcium ion concentration / neuronal cell body membrane / positive regulation of smooth muscle cell migration / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / positive regulation of osteoblast differentiation / positive regulation of defense response to virus by host / coreceptor activity / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / T cell proliferation / cytokine activity / cytokine-mediated signaling pathway / positive regulation of type II interferon production / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / receptor complex / defense response to Gram-positive bacterium / inflammatory response / membrane raft / external side of plasma membrane / innate immune response / signaling receptor binding / neuronal cell body / dendrite / positive regulation of cell population proliferation / cell surface / signal transduction / extracellular space / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Jin Y / Gardner S / Bubeck D | |||||||||
Funding support | United Kingdom, European Union, 2 items
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Citation | Journal: EMBO Rep / Year: 2022 Title: Structural insights into the assembly and activation of the IL-27 signaling complex. Authors: Yibo Jin / Paul K Fyfe / Scott Gardner / Stephan Wilmes / Doryen Bubeck / Ignacio Moraga / Abstract: Interleukin 27 (IL-27) is a heterodimeric cytokine that elicits potent immunosuppressive responses. Comprised of EBI3 and p28 subunits, IL-27 binds GP130 and IL-27Rα receptor chains to activate the ...Interleukin 27 (IL-27) is a heterodimeric cytokine that elicits potent immunosuppressive responses. Comprised of EBI3 and p28 subunits, IL-27 binds GP130 and IL-27Rα receptor chains to activate the JAK/STAT signaling cascade. However, how these receptors recognize IL-27 and form a complex capable of phosphorylating JAK proteins remains unclear. Here, we used cryo electron microscopy (cryoEM) and AlphaFold modeling to solve the structure of the IL-27 receptor recognition complex. Our data show how IL-27 serves as a bridge connecting IL-27Rα (domains 1-2) with GP130 (domains 1-3) to initiate signaling. While both receptors contact the p28 component of the heterodimeric cytokine, EBI3 stabilizes the complex by binding a positively charged surface of IL-27Rα and Domain 1 of GP130. We find that assembly of the IL-27 receptor recognition complex is distinct from both IL-12 and IL-6 cytokine families and provides a mechanistic blueprint for tuning IL-27 pleiotropic actions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14427.map.gz | 1.5 MB | EMDB map data format | |
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Header (meta data) | emd-14427-v30.xml emd-14427.xml | 22.5 KB 22.5 KB | Display Display | EMDB header |
Images | emd_14427.png | 42.9 KB | ||
Others | emd_14427_half_map_1.map.gz emd_14427_half_map_2.map.gz | 32.8 MB 32.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14427 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14427 | HTTPS FTP |
-Validation report
Summary document | emd_14427_validation.pdf.gz | 587.8 KB | Display | EMDB validaton report |
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Full document | emd_14427_full_validation.pdf.gz | 587.4 KB | Display | |
Data in XML | emd_14427_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_14427_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14427 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14427 | HTTPS FTP |
-Related structure data
Related structure data | 7z0lMC 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_14427.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of the IL-27 signalling complex. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: CryoEM half map of the IL-27 signalling complex.
File | emd_14427_half_map_1.map | ||||||||||||
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Annotation | CryoEM half map of the IL-27 signalling complex. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM half map of the IL-27 signalling complex.
File | emd_14427_half_map_2.map | ||||||||||||
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Annotation | CryoEM half map of the IL-27 signalling complex. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : IL-27 Signalling complex
Entire | Name: IL-27 Signalling complex |
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Components |
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-Supramolecule #1: IL-27 Signalling complex
Supramolecule | Name: IL-27 Signalling complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: Interleukin-6 receptor subunit beta
Macromolecule | Name: Interleukin-6 receptor subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 32.91402 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: CGYIYPEFPV VQRGSNFTAI CVLKEACLQH YYVNASYIVW KTNHAAVPRE QVTVINRTTS SVTFTDVVLP SVQLTCNILS FGQIEQNVY GVTMLSGFPP DKPTNLTCIV NEGKNMLCQW DPGRETYLET NYTLKSEWAT EKFPDCQSKH GTSCMVSYMP T YYVNIEVW ...String: CGYIYPEFPV VQRGSNFTAI CVLKEACLQH YYVNASYIVW KTNHAAVPRE QVTVINRTTS SVTFTDVVLP SVQLTCNILS FGQIEQNVY GVTMLSGFPP DKPTNLTCIV NEGKNMLCQW DPGRETYLET NYTLKSEWAT EKFPDCQSKH GTSCMVSYMP T YYVNIEVW VEAENALGKV SSESINFDPV DKVKPTPPYN LSVTNSEELS SILKLSWVSS GLGGLLDLKS DIQYRTKDAS TW IQVPLED TMSPRTSFTV QDLKPFTEYV FRIRSIKDSG KGYWSDWSEE ASGTT |
-Macromolecule #2: Interleukin-27 subunit beta,Interleukin-27 subunit alpha
Macromolecule | Name: Interleukin-27 subunit beta,Interleukin-27 subunit alpha type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 52.475281 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MVSAIVLYVL LAAAAHSAFA GSYTETALVA LSQPRVQCHA SRYPVAVDCS WTPLQAPNST RSTSFIATYR LGVATQQQSQ PCLQRSPQA SRCTIPDVHL FSTVPYMLNV TAVHPGGASS SLLAFVAERI IKPDPPEGVR LRTAGQRLQV LWHPPASWPF P DIFSLKYR ...String: MVSAIVLYVL LAAAAHSAFA GSYTETALVA LSQPRVQCHA SRYPVAVDCS WTPLQAPNST RSTSFIATYR LGVATQQQSQ PCLQRSPQA SRCTIPDVHL FSTVPYMLNV TAVHPGGASS SLLAFVAERI IKPDPPEGVR LRTAGQRLQV LWHPPASWPF P DIFSLKYR LRYRRRGASH FRQVGPIEAT TFTLRNSKPH AKYCIQVSAQ DLTDYGKPSD WSLPGQVESA PHKPRGGGGS GG GGSVESG ENLYFQGFPT DPLSLQELRR EFTVSLYLAR KLLSEVQGYV HSFAESRLPG VNLDLLPLGY HLPNVSLTFQ AWH HLSDSE RLCFLATTLR PFPAMLGGLG TQGTWTSSER EQLWAMRLDL RDLHRHLRFQ VLAAGFKCSK EEEDKEEEEE EEEE EKKLP LGALGGPNQV SSQVSWPQLL YTYQLLHSLE LVLSRAVRDL LLLSLPRRPG SAWDSAAAHH HHHHHH |
-Macromolecule #3: Interleukin-27 receptor subunit alpha
Macromolecule | Name: Interleukin-27 receptor subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 25.968398 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MVSAIVLYVL LAAAAHSAFA GSHGSPGPLQ CYSVGPLGIL NCSWEPLGDL ETPPVLYHQS QKYHPNRVWE VKVPSKQSWV TIPREQFTM ADKLLIWGTQ KGRPLWSSVS VNLETQMKPD TPQIFSQVDI SEEATLEATV QWAPPVWPPQ KVLICQFRYK E CQAETWTR ...String: MVSAIVLYVL LAAAAHSAFA GSHGSPGPLQ CYSVGPLGIL NCSWEPLGDL ETPPVLYHQS QKYHPNRVWE VKVPSKQSWV TIPREQFTM ADKLLIWGTQ KGRPLWSSVS VNLETQMKPD TPQIFSQVDI SEEATLEATV QWAPPVWPPQ KVLICQFRYK E CQAETWTR LEPQLKTDGL TPVEMQNLEP GTCYQVSGRC QVENGYPWGE WSSPLSFQTP FAAAHHHHHH HH |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / 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
Concentration | 0.1 mg/mL | |||||||||
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Buffer | pH: 7.2 Component:
Details: Solutions were made fresh and 0.2um filtered | |||||||||
Grid | Model: EMS Lacey Carbon / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 2s, blot force -2. | |||||||||
Details | 0.8mg/ml |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 2 / Number real images: 56523 / Average exposure time: 3.5 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Initial fitting was performed using Chimera and ChimeraX. Then ISOLDE and Phenix real space refine were used to refine the model. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-7z0l: |