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- EMDB-15899: Cryo-EM structure for the mouse LEPR-CRH2:Leptin:LEPR-Ig complex ... -
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Open data
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Basic information
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Title | Cryo-EM structure for the mouse LEPR-CRH2:Leptin:LEPR-Ig complex following symmetry expansion in combination with local refinement | |||||||||
![]() | Sharpened cryo-EM map following local refinement following symmetry expansion of particle set | |||||||||
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Function / homology | ![]() 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 / negative regulation of glucagon secretion / regulation of endothelial cell proliferation / regulation of natural killer cell proliferation / leptin receptor binding / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / protein-hormone receptor activity / 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 / adult feeding behavior / positive regulation of hepatic stellate cell activation / response to leptin / regulation of nitric-oxide synthase activity / bone mineralization involved in bone maturation / sexual reproduction / regulation of feeding behavior / regulation of lipid biosynthetic process / activation of protein kinase C activity / negative regulation of cartilage development / fatty acid catabolic process / ovulation from ovarian follicle / negative regulation of appetite / positive regulation of developmental growth / leukocyte tethering or rolling / energy reserve metabolic process / regulation of metabolic process / prostaglandin secretion / negative regulation of glucose import / bile acid metabolic process / tyrosine phosphorylation of STAT protein / cellular response to leptin stimulus / hormone metabolic process / regulation of protein localization to nucleus / cardiac muscle hypertrophy / aorta development / intestinal absorption / insulin secretion / regulation of fat cell differentiation / positive regulation of p38MAPK cascade / cytokine receptor activity / peptide hormone receptor binding / negative regulation of vasoconstriction / eating behavior / regulation of gluconeogenesis / glycogen metabolic process / cytokine binding / 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 / peptide hormone binding / regulation of insulin secretion / response to dietary excess / negative regulation of lipid storage / T cell differentiation / positive regulation of TOR signaling / response to vitamin E / glial cell proliferation / regulation of angiogenesis / adipose tissue development / negative regulation of gluconeogenesis / phagocytosis / energy homeostasis / cellular response to retinoic acid / positive regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-12 production / negative regulation of autophagy / cholesterol metabolic process / response to activity / positive regulation of interleukin-8 production / gluconeogenesis / female pregnancy / determination of adult lifespan / positive regulation of receptor signaling pathway via JAK-STAT / regulation of protein phosphorylation / response to insulin / placenta development Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.02 Å | |||||||||
![]() | Verstraete K / Savvides SN / Verschueren KG / Tsirigotaki A | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 324.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.5 KB 26.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 115.5 KB | ||
Masks | ![]() | 343 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() | 169.3 MB 300.2 MB 318.1 MB 318.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b7qMC ![]() 7z3pC ![]() 7z3qC ![]() 7z3rC ![]() 8av2C ![]() 8avbC ![]() 8avcC ![]() 8avdC ![]() 8aveC ![]() 8avfC ![]() 8avoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Sharpened cryo-EM map following local refinement following symmetry expansion of particle set | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.829 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Non-sharpened map following local refinement following symmetry expansion...
File | emd_15899_additional_1.map | ||||||||||||
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Annotation | Non-sharpened map following local refinement following symmetry expansion of particle set | ||||||||||||
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Density Histograms |
-Additional map: Sharpened cryo-EM map with DeepEMhancer
File | emd_15899_additional_2.map | ||||||||||||
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Annotation | Sharpened cryo-EM map with DeepEMhancer | ||||||||||||
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Density Histograms |
-Half map: Half map B
File | emd_15899_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_15899_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Mouse leptin in complex with a trimerized form of the mouse Lep-R...
Entire | Name: Mouse leptin in complex with a trimerized form of the mouse Lep-R extracellular region |
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Components |
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-Supramolecule #1: Mouse leptin in complex with a trimerized form of the mouse Lep-R...
Supramolecule | Name: Mouse leptin in complex with a trimerized form of the mouse Lep-R extracellular region type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 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. |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 444 KDa |
-Macromolecule #1: Leptin
Macromolecule | Name: Leptin / type: protein_or_peptide / ID: 1 Details: Mouse leptin was produced with an N-terminal His-tag and refolded from inclusion bodies produced in E. coli Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 18.873283 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSSHHHHHH PGGPGSENLY FQGGSTGGVP IQKVQDDTKT LIKTIVTRIN DISHTQSVSA KQRVTGLDFI PGLHPILSLS KMDQTLAVY QQVLTSLPSQ NVLQIANDLE NLRDLLHLLA FSKSCSLPQT SGLQKPESLD GVLEASLYST EVVALSRLQG S LQDILQQL DVSPEC |
-Macromolecule #2: Leptin receptor
Macromolecule | Name: Leptin receptor / type: protein_or_peptide / ID: 2 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. Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 97.479391 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: LNLAYPISPW KFKLFCGPPN TTDDSFLSPA GAPNNASALK GASEAIVEAK FNSSGIYVPE LSKTVFHCCF GNEQGQNCSA LTDNTEGKT LASVVKASVF RQLGVNWDIE CWMKGDLTLF ICHMEPLPKN PFKNYDSKVH LLYDLPEVID DSPLPPLKDS F QTVQCNCS ...String: LNLAYPISPW KFKLFCGPPN TTDDSFLSPA GAPNNASALK GASEAIVEAK FNSSGIYVPE LSKTVFHCCF GNEQGQNCSA LTDNTEGKT LASVVKASVF RQLGVNWDIE CWMKGDLTLF ICHMEPLPKN PFKNYDSKVH LLYDLPEVID DSPLPPLKDS F QTVQCNCS LRGCECHVPV PRAKLNYALL MYLEITSAGV SFQSPLMSLQ PMLVVKPDPP LGLHMEVTDD GNLKISWDSQ TM APFPLQY QVKYLENSTI VREAAEIVSA TSLLVDSVLP GSSYEVQVRS KRLDGSGVWS DWSSPQVFTT QDVVYFPPKI LTS VGSNAS FHCIYKNENQ IISSKQIVWW RNLAEKIPEI QYSIVSDRVS KVTFSNLKAT RPRGKFTYDA VYCCNEQACH HRYA ELYVI DVNINISCET DGYLTKMTCR WSPSTIQSLV GSTVQLRYHR RSLYCPDSPS IHPTSEPKNC VLQRDGFYEC VFQPI FLLS GYTMWIRINH SLGSLDSPPT CVLPDSVVKP LPPSNVKAEI TVNTGLLKVS WEKPVFPENN LQFQIRYGLS GKEIQW KTH EVFDAKSKSA SLLVSDLCAV YVVQVRCRRL DGLGYWSNWS SPAYTLVMDV KVPMRGPEFW RKMDGDVTKK ERNVTLL WK PLTKNDSLCS VRRYVVKHRT AHNGTWSEDV GNRTNLTFLW TEPAHTVTVL AVNSLGASLV NFNLTFSWPM SKVSAVES L SAYPLSSSCV ILSWTLSPDD YSLLYLVIEW KILNEDDGMK WLRIPSNVKK FYIHDNFIPI EKYQFSLYPV FMEGVGKPK IINGFTKDAI DKQQNDAGST GGSGGSGGSG GSGGSRMKQI EDKIEEILSK IYHIENEIAR IKKLIGER |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 1 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: 20 mM HEPES, 150 mM NaCl, pH 7.4 | |||||||||
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 295 K / Instrument: LEICA EM GP | |||||||||
Details | This sample was monodisperse. |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 13230 / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Software | Name: ![]() |
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Details | The crystallographic model for the mLEP-RCRH2:mLeptin:mLEP-R_IgCRH2' complex (pdb 7z3r) was fitted in the cryo-EM map using Chimera and real-space refined in Phenix using reference restraints to the starting model. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-8b7q: |