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- EMDB-15677: Cryo-EM structure for mouse leptin in complex with the mouse LEP-... -
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Open data
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Basic information
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Title | Cryo-EM structure for mouse leptin in complex with the mouse LEP-R ectodomain (1:2 mLEP:mLEPR model) | |||||||||
![]() | Sharpened cryo-EM map following non-uniform refinement | |||||||||
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![]() | leptin / LEP-R / obesity / metabolism / energy balance / CYTOKINE | |||||||||
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: 4.43 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 | ![]() | 38.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.7 KB 23.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.3 KB | Display | ![]() |
Images | ![]() | 101.8 KB | ||
Masks | ![]() | 40.6 MB | ![]() | |
Others | ![]() ![]() ![]() | 20.4 MB 37.7 MB 37.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 813.5 KB | Display | ![]() |
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Full document | ![]() | 813.1 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8avbMC ![]() 7z3pC ![]() 7z3qC ![]() 7z3rC ![]() 8av2C ![]() 8avcC ![]() 8avdC ![]() 8aveC ![]() 8avfC ![]() 8avoC ![]() 8b7qC 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 non-uniform refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.51 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 cryo-EM map following non-uniform refinement
File | emd_15677_additional_1.map | ||||||||||||
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Annotation | Non-sharpened cryo-EM map following non-uniform refinement | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_15677_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
-Half map: Half map B
File | emd_15677_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Complex between mouse leptin and the mouse LEP-R ectodomain.
Entire | Name: Complex between mouse leptin and the mouse LEP-R ectodomain. |
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Components |
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-Supramolecule #1: Complex between mouse leptin and the mouse LEP-R ectodomain.
Supramolecule | Name: Complex between mouse leptin and the mouse LEP-R ectodomain. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The mouse leptin:LEP-R complex was isolated from the excess of mouse leptin via size-exclusion chromatography. The elution peak corresponding to the leptin:LEP-R was concentrated to 5 mg/mL, ...Details: The mouse leptin:LEP-R complex was isolated from the excess of mouse leptin via size-exclusion chromatography. The elution peak corresponding to the leptin:LEP-R was concentrated to 5 mg/mL, aliquoted and flash frozen into liquid nitrogen. Just before plunge freezing the sample was diluted to 0.2 mg/mL. |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 230 KDa |
-Macromolecule #1: Leptin
Macromolecule | Name: Leptin / type: protein_or_peptide / ID: 1 Details: Mouse leptin was expressed with an N-terminal His-tag. Before complex formation with the mouse LEP-R ecotodomain, the His-tag was removed with TEV protease Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 16.434676 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GGSTGGVPIQ KVQDDTKTLI KTIVTRINDI SHTQSVSAKQ RVTGLDFIPG LHPILSLSKM DQTLAVYQQV LTSLPSQNVL QIANDLENL RDLLHLLAFS KSCSLPQTSG LQKPESLDGV LEASLYSTEV VALSRLQGSL QDILQQLDVS PEC UniProtKB: Leptin |
-Macromolecule #2: Leptin receptor
Macromolecule | Name: Leptin receptor / type: protein_or_peptide / ID: 2 Details: The N-terminally His-tagged LEP-R ecotomain was secreted from HEK293 FreeStyle cells. The N-terminal His-tag was not removed before complex formation with refolded mouse leptin. Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 94.081344 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AHHHHHHPGG PGSDELDLNL AYPISPWKFK LFCGPPNTTD DSFLSPAGAP NNASALKGAS EAIVEAKFNS SGIYVPELSK TVFHCCFGN EQGQNCSALT DNTEGKTLAS VVKASVFRQL GVNWDIECWM KGDLTLFICH MEPLPKNPFK NYDSKVHLLY D LPEVIDDS ...String: AHHHHHHPGG PGSDELDLNL AYPISPWKFK LFCGPPNTTD DSFLSPAGAP NNASALKGAS EAIVEAKFNS SGIYVPELSK TVFHCCFGN EQGQNCSALT DNTEGKTLAS VVKASVFRQL GVNWDIECWM KGDLTLFICH MEPLPKNPFK NYDSKVHLLY D LPEVIDDS PLPPLKDSFQ TVQCNCSLRG CECHVPVPRA KLNYALLMYL EITSAGVSFQ SPLMSLQPML VVKPDPPLGL HM EVTDDGN LKISWDSQTM APFPLQYQVK YLENSTIVRE AAEIVSATSL LVDSVLPGSS YEVQVRSKRL DGSGVWSDWS SPQ VFTTQD VVYFPPKILT SVGSNASFHC IYKNENQIIS SKQIVWWRNL AEKIPEIQYS IVSDRVSKVT FSNLKATRPR GKFT YDAVY CCNEQACHHR YAELYVIDVN INISCETDGY LTKMTCRWSP STIQSLVGST VQLRYHRRSL YCPDSPSIHP TSEPK NCVL QRDGFYECVF QPIFLLSGYT MWIRINHSLG SLDSPPTCVL PDSVVKPLPP SNVKAEITVN TGLLKVSWEK PVFPEN NLQ FQIRYGLSGK EIQWKTHEVF DAKSKSASLL VSDLCAVYVV QVRCRRLDGL GYWSNWSSPA YTLVMDVKVP MRGPEFW RK MDGDVTKKER NVTLLWKPLT KNDSLCSVRR YVVKHRTAHN GTWSEDVGNR TNLTFLWTEP AHTVTVLAVN SLGASLVN F NLTFSWPMSK VSAVESLSAY PLSSSCVILS WTLSPDDYSL LYLVIEWKIL NEDDGMKWLR IPSNVKKFYI HDNFIPIEK YQFSLYPVFM EGVGKPKIIN GFTKDAIDKQ QNDAG UniProtKB: Leptin receptor |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: 20 mM Hepes, 150 mM NaCl, pH 7.4 | |||||||||
Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 1 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | The mouse leptin:LEP-R complex was isolated from the excess of mouse leptin via size-exclusion chromatography. The elution peak corresponding to the leptin:LEP-R was concentrated to 5 mg/mL, aliquoted and flash frozen into liquid nitrogen. Just before plunge freezing the sample was diluted to 0.2 mg/mL. |
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Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7100 / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | An atomic model for a 1:2 mLeptin:LEP-RIgCRH2FnIII complex was created based on the AlphaFold prediction for mLEP-RECD and the determined mLeptin:mLEP-RIgCRH2 and mLEP-RFnIII module crystal structures and fitted in the cryo-EM map via Chimera followed by real space refinement in Phenix using rigid body refinement and coordinate refinement with reference restraints to the starting model and hydrogen-bonding restraints across the site II and site III mLeptin:mLEP-R interface regions. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-8avb: |