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Open data
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Basic information
Entry | Database: PDB / ID: 7z0l | |||||||||
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Title | IL-27 signalling complex | |||||||||
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![]() | CYTOKINE / immunosuppression / EBI3 / IL-27R-alpha / gp130 / p28. | |||||||||
Function / homology | ![]() interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / negative regulation of T cell extravasation / negative regulation of cellular extravasation / negative regulation of T-helper 17 type immune response / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / oncostatin-M receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation ...interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / negative regulation of T cell extravasation / negative regulation of cellular extravasation / negative regulation of T-helper 17 type immune response / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / oncostatin-M receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / Interleukin-6 signaling / Interleukin-35 Signalling / interleukin-27 receptor activity / negative regulation of type 2 immune response / oncostatin-M receptor complex / regulation of isotype switching to IgG isotypes / ciliary neurotrophic factor receptor binding / interleukin-6 receptor activity / interleukin-6 binding / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / leptin-mediated signaling pathway / interleukin-6 receptor complex / response to Gram-positive bacterium / regulation of Notch signaling pathway / interleukin-6 receptor binding / positive regulation of T-helper 1 type immune response / interleukin-11-mediated signaling pathway / positive regulation of astrocyte differentiation / intestinal epithelial cell development / interleukin-12 receptor complex / interleukin-23 receptor complex / negative regulation of interleukin-17 production / cytokine receptor activity / glycogen metabolic process / neuronal cell body membrane / interleukin-6-mediated signaling pathway / regulation of T cell proliferation / positive regulation of Notch signaling pathway / negative regulation of cytosolic calcium ion concentration / protein tyrosine kinase activator activity / cytokine binding / positive regulation of activated T cell proliferation / positive regulation of smooth muscle cell migration / peptide hormone binding / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / positive regulation of osteoblast differentiation / coreceptor activity / T cell proliferation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||
![]() | Jin, Y. / Gardner, S. / Bubeck, D. | |||||||||
Funding support | ![]()
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 358.8 KB | Display | ![]() |
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PDB format | ![]() | 246.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 35.1 KB | Display | |
Data in CIF | ![]() | 50.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 14427MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 32914.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 52475.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Protein | Mass: 25968.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Sugar | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: IL-27 Signalling complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.1 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||
Buffer solution | pH: 7.2 / Details: Solutions were made fresh and 0.2um filtered | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.8mg/ml | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: Blot time 2s, blot force -2 |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 56523 |
Image scans | Width: 4092 / Height: 5760 |
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Processing
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EM software |
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CTF correction | Details: CTF correction was performed following 3D reconstruction. Local CTF refinement was carried out during refinement Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1811398 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208431 / Algorithm: BACK PROJECTION Details: Final reconstruction was performed using local refinement in cryoSPARC. Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: Initial fitting was performed using Chimera and ChimeraX. Then ISOLDE and Phenix real space refine were used to refine the model. | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 195.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
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