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- PDB-8avb: Cryo-EM structure for mouse leptin in complex with the mouse LEP-... -

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Basic information

Entry
Database: PDB / ID: 8avb
TitleCryo-EM structure for mouse leptin in complex with the mouse LEP-R ectodomain (1:2 mLEP:mLEPR model).
Components
  • Leptin
  • Leptin receptor
KeywordsCYTOKINE / leptin / LEP-R / obesity / metabolism / energy balance
Function / homology
Function and homology information


Synthesis, secretion, and deacylation of Ghrelin / 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 / regulation of transport / negative regulation of appetite by leptin-mediated signaling pathway / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of glucagon secretion ...Synthesis, secretion, and deacylation of Ghrelin / 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 / regulation of transport / negative regulation of appetite by leptin-mediated signaling pathway / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of glucagon secretion / regulation of endothelial cell proliferation / regulation of natural killer cell mediated cytotoxicity / regulation of natural killer cell proliferation / leptin receptor binding / bone growth / positive regulation of luteinizing hormone secretion / regulation of natural killer cell activation / glycerol biosynthetic process / elastin metabolic process / leptin-mediated signaling pathway / positive regulation of hepatic stellate cell activation / positive regulation of follicle-stimulating hormone secretion / regulation of steroid biosynthetic process / positive regulation of monoatomic ion transport / regulation of intestinal cholesterol absorption / regulation of bone remodeling / regulation of brown fat cell differentiation / positive regulation of peroxisome proliferator activated receptor signaling pathway / regulation of nitric-oxide synthase activity / adult feeding behavior / response to leptin / activation of protein kinase C activity / bone mineralization involved in bone maturation / regulation of lipid biosynthetic process / sexual reproduction / negative regulation of cartilage development / regulation of feeding behavior / 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 / cellular response to leptin stimulus / negative regulation of D-glucose import / prostaglandin secretion / regulation of protein localization to nucleus / cardiac muscle hypertrophy / hormone metabolic process / positive regulation of p38MAPK cascade / intestinal absorption / regulation of fat cell differentiation / insulin secretion / regulation of metabolic process / aorta development / negative regulation of vasoconstriction / regulation of gluconeogenesis / peptide hormone receptor binding / glycogen metabolic process / eating behavior / fatty acid beta-oxidation / regulation of cytokine production involved in inflammatory response / central nervous system neuron development / response to dietary excess / negative regulation of lipid storage / T cell differentiation / response to vitamin E / cell surface receptor signaling pathway via JAK-STAT / positive regulation of TOR signaling / regulation of angiogenesis / adipose tissue development / negative regulation of gluconeogenesis / phagocytosis / glial cell proliferation / positive regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / energy homeostasis / cellular response to retinoic acid / positive regulation of interleukin-12 production / regulation of insulin secretion / negative regulation of autophagy / cholesterol metabolic process / response to activity / gluconeogenesis / positive regulation of interleukin-8 production / female pregnancy / positive regulation of receptor signaling pathway via JAK-STAT / determination of adult lifespan / response to insulin / placenta development / hormone activity / regulation of blood pressure / lipid metabolic process / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / cellular response to insulin stimulus / glucose metabolic process / circadian rhythm / positive regulation of reactive oxygen species metabolic process / positive regulation of tumor necrosis factor production
Similarity search - Function
Leptin / Leptin / Leptin receptor, immunoglobulin-like domain / Obesity receptor immunoglobulin like domain / Short hematopoietin receptor, family 1, conserved site / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Four-helical cytokine-like, core ...Leptin / Leptin / Leptin receptor, immunoglobulin-like domain / Obesity receptor immunoglobulin like domain / Short hematopoietin receptor, family 1, conserved site / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Four-helical cytokine-like, core / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Leptin / Leptin receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.43 Å
AuthorsVerstraete, K. / Savvides, S.N. / Verschueren, K.G. / Tsirigotaki, A.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0619N Belgium
CitationJournal: 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
DepositionAug 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 24, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jul 26, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.pdb_format_compatible
Revision 1.4Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leptin
B: Leptin receptor
F: Leptin receptor


Theoretical massNumber of molelcules
Total (without water)204,5973
Polymers204,5973
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SEC-MALLS experiments show that mouse leptin and the mouse LEP-R ectodomain form a higher-order complex in a concentration-dependent and reversible manner. At 5 mg/mL (40 ...Evidence: light scattering, SEC-MALLS experiments show that mouse leptin and the mouse LEP-R ectodomain form a higher-order complex in a concentration-dependent and reversible manner. At 5 mg/mL (40 micromolar) the leptin:LEP-R complex elutes as complex with an apparent protein molecular weight of 229 kDa, which would correspond to a 2:2 stoichiometry.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Leptin / Obesity factor


Mass: 16434.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lep, Ob / Plasmid: pET15b / Details (production host): pET15b_His_TEV_mLEP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41160
#2: Protein Leptin receptor / LEP-R / B219 / OB receptor / OB-R


Mass: 94081.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lepr, Db, Obr / Plasmid: pCAGGS / Details (production host): pCAGGS_ss_His_Casp_mLepR / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): FreeStyle / References: UniProt: P48356
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex between mouse leptin and the mouse LEP-R ectodomain.
Type: COMPLEX
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.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.230 MDa / Experimental value: YES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human) / Strain: Freestyle / Plasmid: pCAGGS
Buffer solutionpH: 7.4 / Details: 20 mM Hepes, 150 mM NaCl, pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMHepesC8H18N2O4S1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7100

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARCv3.3.2particle selectionBlob picker, TOPAZ, template picking
4cryoSPARCv3.3.2CTF correctionPatch CTF
7UCSF Chimera1.17model fitting
9PHENIX1.19.2model refinementPhenix real space refine
10cryoSPARCv3.3.2initial Euler assignmentAb initio
11cryoSPARCv3.3.2final Euler assignmentNon-uniform refinement
13cryoSPARCv3.3.23D reconstructionNon-uniform refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 28684
Details: Movies were motion corrected via MotionCor2 1.4.0 and had their contrast transfer functions (CTFs) determined via patch-based CTF estimation ain cryoSPARC v3.3.2. Initial high-resolution 2D ...Details: Movies were motion corrected via MotionCor2 1.4.0 and had their contrast transfer functions (CTFs) determined via patch-based CTF estimation ain cryoSPARC v3.3.2. Initial high-resolution 2D classes were obtained via the blob picker function and reference-free 2D classification in cryoSPARC, These 2D classes were then used to seed template-based and neural network-based particle picking via Topaz 0.2.4. Junk particles were removed by multiple rounds of 2D classification. High-resolution 2D classes corresponding to an apparent dimeric mLeptin:mLEP-R were manually selected.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28296 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
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 ...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.
Atomic model buildingPDB-ID: 7Z3R

7z3r


Accession code: 7Z3R / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 509.52 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004710869
ELECTRON MICROSCOPYf_angle_d0.777714817
ELECTRON MICROSCOPYf_chiral_restr0.04961678
ELECTRON MICROSCOPYf_plane_restr0.00611863
ELECTRON MICROSCOPYf_dihedral_angle_d5.47291433

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