[English] 日本語
Yorodumi- PDB-8avd: Cryo-EM structure for a 3:3 complex between mouse leptin and the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8avd | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure for a 3:3 complex between mouse leptin and the mouse LEP-R ectodomain (local refinement) | ||||||
Components |
| ||||||
Keywords | CYTOKINE / leptin / LEP-R / obesity / metabolism / energy balance | ||||||
Function / homology | Function and homology information negative regulation of metabolic process / negative regulation of locomotor rhythm / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of eating behavior / regulation of lipoprotein lipid oxidation / cellular response to L-ascorbic acid / positive regulation of fat cell apoptotic process / negative regulation of glutamine transport / leptin receptor activity / negative regulation of appetite by leptin-mediated signaling pathway ...negative regulation of metabolic process / negative regulation of locomotor rhythm / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of eating behavior / regulation of lipoprotein lipid oxidation / cellular response to L-ascorbic acid / positive regulation of fat cell apoptotic process / negative regulation of glutamine transport / leptin receptor activity / negative regulation of appetite by leptin-mediated signaling pathway / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / protein-hormone receptor activity / negative regulation of glucagon secretion / regulation of endothelial cell proliferation / regulation of natural killer cell proliferation / leptin receptor binding / positive regulation of luteinizing hormone secretion / regulation of natural killer cell mediated cytotoxicity / bone growth / regulation of natural killer cell activation / positive regulation of monoatomic ion transport / glycerol biosynthetic process / elastin metabolic process / leptin-mediated signaling pathway / positive regulation of follicle-stimulating hormone secretion / regulation of steroid biosynthetic process / regulation of intestinal cholesterol absorption / regulation of bone remodeling / regulation of brown fat cell differentiation / positive regulation of peroxisome proliferator activated receptor signaling pathway / positive regulation of hepatic stellate cell activation / response to leptin / adult feeding behavior / regulation of nitric-oxide synthase activity / bone mineralization involved in bone maturation / sexual reproduction / regulation of lipid biosynthetic process / regulation of feeding behavior / activation of protein kinase C activity / fatty acid catabolic process / negative regulation of cartilage development / ovulation from ovarian follicle / negative regulation of appetite / positive regulation of developmental growth / leukocyte tethering or rolling / energy reserve metabolic process / bile acid metabolic process / negative regulation of glucose import / prostaglandin secretion / tyrosine phosphorylation of STAT protein / cellular response to leptin stimulus / regulation of protein localization to nucleus / regulation of metabolic process / cardiac muscle hypertrophy / hormone metabolic process / aorta development / negative regulation of lipid storage / cytokine receptor activity / insulin secretion / intestinal absorption / regulation of fat cell differentiation / positive regulation of p38MAPK cascade / peptide hormone receptor binding / negative regulation of vasoconstriction / eating behavior / regulation of gluconeogenesis / glycogen metabolic process / fatty acid beta-oxidation / central nervous system neuron development / regulation of cytokine production involved in inflammatory response / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cytokine binding / peptide hormone binding / regulation of insulin secretion / response to dietary excess / T cell differentiation / positive regulation of TOR signaling / response to vitamin E / glial cell proliferation / regulation of angiogenesis / negative regulation of gluconeogenesis / adipose tissue development / phagocytosis / positive regulation of insulin receptor signaling pathway / cellular response to retinoic acid / positive regulation of T cell proliferation / energy homeostasis / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-12 production / cholesterol metabolic process / negative regulation of autophagy / response to activity / positive regulation of interleukin-8 production / placenta development / gluconeogenesis / female pregnancy / determination of adult lifespan / lipid metabolic process / positive regulation of receptor signaling pathway via JAK-STAT / regulation of protein phosphorylation Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.42 Å | ||||||
Authors | Verstraete, K. / Savvides, S.N. / Verschueren, K.G. / Tsirigotaki, A. | ||||||
Funding support | Belgium, 1items
| ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Mechanism of receptor assembly via the pleiotropic adipokine Leptin. Authors: Alexandra Tsirigotaki / Ann Dansercoer / Koen H G Verschueren / Iva Marković / Christoph Pollmann / Maximillian Hafer / Jan Felix / Catherine Birck / Wouter Van Putte / Dominiek Catteeuw / ...Authors: Alexandra Tsirigotaki / Ann Dansercoer / Koen H G Verschueren / Iva Marković / Christoph Pollmann / Maximillian Hafer / Jan Felix / Catherine Birck / Wouter Van Putte / Dominiek Catteeuw / Jan Tavernier / J Fernando Bazan / Jacob Piehler / Savvas N Savvides / Kenneth Verstraete / Abstract: The adipokine Leptin activates its receptor LEP-R in the hypothalamus to regulate body weight and exerts additional pleiotropic functions in immunity, fertility and cancer. However, the structure and ...The adipokine Leptin activates its receptor LEP-R in the hypothalamus to regulate body weight and exerts additional pleiotropic functions in immunity, fertility and cancer. However, the structure and mechanism of Leptin-mediated LEP-R assemblies has remained unclear. Intriguingly, the signaling-competent isoform of LEP-R is only lowly abundant amid several inactive short LEP-R isoforms contributing to a mechanistic conundrum. Here we show by X-ray crystallography and cryo-EM that, in contrast to long-standing paradigms, Leptin induces type I cytokine receptor assemblies featuring 3:3 stoichiometry and demonstrate such Leptin-induced trimerization of LEP-R on living cells via single-molecule microscopy. In mediating these assemblies, Leptin undergoes drastic restructuring that activates its site III for binding to the Ig domain of an adjacent LEP-R. These interactions are abolished by mutations linked to obesity. Collectively, our study provides the structural and mechanistic framework for how evolutionarily conserved Leptin:LEP-R assemblies with 3:3 stoichiometry can engage distinct LEP-R isoforms to achieve signaling. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8avd.cif.gz | 398.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8avd.ent.gz | 290.3 KB | Display | PDB format |
PDBx/mmJSON format | 8avd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8avd_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8avd_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8avd_validation.xml.gz | 59.1 KB | Display | |
Data in CIF | 8avd_validation.cif.gz | 87 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/8avd ftp://data.pdbj.org/pub/pdb/validation_reports/av/8avd | HTTPS FTP |
-Related structure data
Related structure data | 15679MC 7z3pC 7z3qC 7z3rC 8av2C 8avbC 8avcC 8aveC 8avfC 8avoC 8b7qC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 18873.283 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Mouse leptin was produced with an N-terminal His-tag and refolded from inclusion bodies produced in E. coli Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lep, Ob / Plasmid: pET15b / Details (production host): pET15b-His-TEV-mLeptin / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41160 #2: Protein | Mass: 97479.391 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: The mLEP-R ectodomain was C-terminally fused to a trimeric GCN4 isoleucine zipper tag and secreted from HEK93 FreeStyle cells and complexed with refolded mouse leptin produced in E.coli. Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lepr, Db, Obr / Plasmid: pTwist / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): FreeStyle / References: UniProt: P48356 #3: Chemical | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Stucture of mouse leptin in complex with a trimerized form of the mouse Lep-R extracellular region Type: COMPLEX Details: The mLEP-R ectodomain was C-terminally fused to a trimeric GCN4 isoleucine zipper tag and secreted from HEK93 FreeStyle cells and complexed with refolded mouse leptin produced in E.coli. Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.444 MDa / Experimental value: YES | |||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Strain: 293 Freestyle / Plasmid: pTwist | |||||||||||||||
Buffer solution | pH: 7.4 / Details: 20 mM HEPES, 150 mM NaCl, pH 7.4 | |||||||||||||||
Buffer component |
| |||||||||||||||
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13230 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 141157 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54708 Details: The final map was obtained via local refinement in cryoSPARC using a mask around the mouse leptin:LEP-R core region of the trimeric complex Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7Z3R | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 240.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|