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Yorodumi- PDB-8pb1: Cryo-EM structure of a pre-dimerized murine IL-12 complete extrac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pb1 | |||||||||
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Title | Cryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling complex (Class 1), obtained after local refinement. | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Complex / Cytokine / Receptor | |||||||||
Function / homology | Function and homology information interleukin-12 beta subunit binding / Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / Interleukin-35 Signalling / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / T-helper 1 cell activation / natural killer cell activation involved in immune response ...interleukin-12 beta subunit binding / Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / Interleukin-35 Signalling / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / T-helper 1 cell activation / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / cellular response to hydroperoxide / positive regulation of T-helper 1 type immune response / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / positive regulation of smooth muscle cell apoptotic process / interleukin-12 receptor binding / natural killer cell activation / T-helper cell differentiation / interleukin-23 receptor complex / defense response to tumor cell / positive regulation of osteoclast differentiation / negative regulation of interleukin-17 production / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / response to UV-B / regulation of NMDA receptor activity / CaM pathway / positive regulation of natural killer cell proliferation / Cam-PDE 1 activation / positive regulation of granulocyte macrophage colony-stimulating factor production / Sodium/Calcium exchangers / syntaxin-1 binding / Calmodulin induced events / positive regulation of T cell differentiation / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / cytokine receptor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / calcium/calmodulin-dependent protein kinase activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / negative regulation of interleukin-10 production / positive regulation of ryanodine-sensitive calcium-release channel activity / cytokine binding / positive regulation of activated T cell proliferation / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / defense response to protozoan / positive regulation of interleukin-17 production / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / Ion transport by P-type ATPases / positive regulation of interleukin-10 production / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / extrinsic apoptotic signaling pathway via death domain receptors / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / immunoglobulin mediated immune response / negative regulation of protein secretion / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / coreceptor activity / positive regulation of autophagy / eNOS activation / T cell proliferation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Felix, J. / Bloch, Y. / Savvides, S.N. | |||||||||
Funding support | Belgium, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23. Authors: Yehudi Bloch / Jan Felix / Romain Merceron / Mathias Provost / Royan Alipour Symakani / Robin De Backer / Elisabeth Lambert / Ahmad R Mehdipour / Savvas N Savvides / Abstract: Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into ...Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into their complete extracellular assemblies. Furthermore, there is a paucity of structural details describing the IL-12-receptor interaction interfaces, in contrast to IL-23-receptor complexes. Here we report structures of fully assembled mouse IL-12/human IL-23-receptor complexes comprising the complete extracellular segments of the cognate receptors determined by electron cryo-microscopy. The structures reveal key commonalities but also surprisingly diverse features. Most notably, whereas IL-12 and IL-23 both utilize a conspicuously presented aromatic residue on their α-subunit as a hotspot to interact with the N-terminal Ig domain of their high-affinity receptors, only IL-12 juxtaposes receptor domains proximal to the cell membrane. Collectively, our findings will help to complete our understanding of cytokine-mediated assemblies of tall cytokine receptors and will enable a cytokine-specific interrogation of IL-12/IL-23 signaling in physiology and disease. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pb1.cif.gz | 188 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pb1.ent.gz | 131.2 KB | Display | PDB format |
PDBx/mmJSON format | 8pb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pb1_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8pb1_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8pb1_validation.xml.gz | 46 KB | Display | |
Data in CIF | 8pb1_validation.cif.gz | 65.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/8pb1 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/8pb1 | HTTPS FTP |
-Related structure data
Related structure data | 17580MC 8c7mC 8cr5C 8cr6C 8cr8C 8odxC 8odzC 8oe0C 8oe4C 8ppmC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Interleukin-12 subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 25927.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12a / Cell line (production host): HEK293S MGAT-/- / Production host: Homo sapiens (human) / References: UniProt: P43431 |
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#2: Protein | Mass: 35837.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12b / Cell line (production host): HEK293S MGAT -/- / Production host: Homo sapiens (human) / References: UniProt: P43432 |
-Interleukin-12 receptor subunit beta- ... , 2 types, 2 molecules CD
#3: Protein | Mass: 63789.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12rb1, Il12rb, DAPK1, DAPK / Cell line (production host): HEK293S MGAT-/- / Production host: Homo sapiens (human) References: UniProt: Q60837, UniProt: P53355, non-specific serine/threonine protein kinase |
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#4: Protein | Mass: 85723.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12rb2, CALM1, CALM, CAM, CAM1 / Cell line (production host): HEK293S MGAT -/- / Production host: Homo sapiens (human) / References: UniProt: P97378, UniProt: P0DP23 |
-Sugars , 2 types, 5 molecules
#5: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 1 molecules
#7: Water | ChemComp-HOH / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Murine IL-12 in complex with mIL-12Rbeta1-DAPK1 and mIL-12Rbeta2-Calmodulin. Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.216 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Buffer solution | pH: 7.4 Details: HEPES-buffered saline (HBS) with added calcium chloride: 25 mM HEPES, pH 7.4, 150 mM NaCl, 5 mM CaCl | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Details: Leica EM GP2, 5 s. blotting time. |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 3.37 sec. / Electron dose: 61.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 8145 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2151468 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268498 Details: The final map was obtained after performing a local refinement in cryoSPARC, using a mask around mIL-12 in complex with D1-D2 of mIL12Rbeta1 and D1-D2 of mIL-12Rbeta2. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.26 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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