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Yorodumi- PDB-8cr5: Murine Interleukin-12 receptor beta 1 domain 1 in complex with mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cr5 | |||||||||
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Title | Murine Interleukin-12 receptor beta 1 domain 1 in complex with murine Interleukin-12 beta. | |||||||||
Components |
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Keywords | CYTOKINE / complex / inflammation / glycoprotein / immunity | |||||||||
Function / homology | Function and homology information Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / 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 ...Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / 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 / positive regulation of T-helper 1 type immune response / positive regulation of smooth muscle cell apoptotic process / natural killer cell activation / T-helper cell differentiation / interleukin-23 receptor complex / positive regulation of osteoclast differentiation / negative regulation of interleukin-17 production / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / response to UV-B / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / cytokine receptor activity / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / defense response to protozoan / positive regulation of interleukin-17 production / cytokine binding / positive regulation of interleukin-10 production / immunoglobulin mediated immune response / negative regulation of protein secretion / 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 / negative regulation of inflammatory response to antigenic stimulus / positive regulation of interleukin-12 production / : / cytokine activity / endosome lumen / negative regulation of smooth muscle cell proliferation / growth factor activity / cytokine-mediated signaling pathway / cellular response to type II interferon / Golgi lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cell migration / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to virus / cell population proliferation / cell surface receptor signaling pathway / receptor complex / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / protein-containing complex binding / cell surface / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Merceron, R. / Bloch, Y. / Felix, J. / 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 | 8cr5.cif.gz | 210.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cr5.ent.gz | 146.5 KB | Display | PDB format |
PDBx/mmJSON format | 8cr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cr5_validation.pdf.gz | 806.6 KB | Display | wwPDB validaton report |
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Full document | 8cr5_full_validation.pdf.gz | 816.2 KB | Display | |
Data in XML | 8cr5_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 8cr5_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/8cr5 ftp://data.pdbj.org/pub/pdb/validation_reports/cr/8cr5 | HTTPS FTP |
-Related structure data
Related structure data | 8c7mC 8cr6C 8cr8C 8odxC 8odzC 8oe0C 8oe4C 8pb1C 8ppmC C: citing same article (ref.) |
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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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Unit cell |
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-Components
#1: Protein | Mass: 39382.527 Da / Num. of mol.: 1 / Mutation: C197S Source method: isolated from a genetically manipulated source Details: residues [M1-A22] encode the signal peptide which is most likely removed during translation/folding. residues [G336-H343] encode for cloning scar and purification tag. Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12b / Plasmid: pHLsec / Cell line (production host): HEK293S MGAT1-/- / Production host: Homo sapiens (human) / References: UniProt: P43432 |
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#2: Protein | Mass: 29611.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues [M1-C19] encode the signal peptide which is most likely removed during translation/folding. Residues [G259-H266] encode a cloning scar and purification tag. Serendipitous in-drop ...Details: Residues [M1-C19] encode the signal peptide which is most likely removed during translation/folding. Residues [G259-H266] encode a cloning scar and purification tag. Serendipitous in-drop proteolysis removed the C-terminal half of the protein. Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12rb1, Il12rb / Plasmid: pHLsec / Cell line (production host): HEK293S MGat1-/- / Production host: Homo sapiens (human) / References: UniProt: Q60837 |
#3: 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 |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: (BCS E4) 20% PEG smear medium, 0.1M MgCl2, 0.1 M KCl, 0.1M PIPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.008 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→165 Å / Num. obs: 26490 / % possible obs: 99.5 % / Redundancy: 3.558 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.172 / Net I/σ(I): 7.18 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 3.687 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 1969 / CC1/2: 0.641 / Rrim(I) all: 1.312 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→49.48 Å / SU ML: 0.3377 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.7455 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→49.48 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1
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