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- PDB-8avc: Mouse leptin:LEP-R complex cryoEM structure (3:3 model) -

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Basic information

Entry
Database: PDB / ID: 8avc
TitleMouse leptin:LEP-R complex cryoEM structure (3:3 model)
Components
  • Leptin
  • Leptin receptor
KeywordsCYTOKINE / leptin / LEP-R / obesity / metabolism / energy balance
Function / homology
Function and homology information


negative regulation of locomotor rhythm / negative regulation of metabolic process / positive regulation of protein modification process / regulation of intestinal cholesterol absorption / Synthesis, secretion, and deacylation of Ghrelin / leptin receptor activity / regulation of lipoprotein lipid oxidation / cellular response to L-ascorbic acid / positive regulation of fat cell apoptotic process / negative regulation of glutamine transport ...negative regulation of locomotor rhythm / negative regulation of metabolic process / positive regulation of protein modification process / regulation of intestinal cholesterol absorption / Synthesis, secretion, and deacylation of Ghrelin / leptin receptor activity / regulation of lipoprotein lipid oxidation / cellular response to L-ascorbic acid / positive regulation of fat cell apoptotic process / negative regulation of glutamine transport / activation of protein kinase C activity / negative regulation of appetite by leptin-mediated signaling pathway / negative regulation of eating behavior / positive regulation of luteinizing hormone secretion / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of glucagon secretion / regulation of steroid biosynthetic process / negative regulation of cartilage development / elastin metabolic process / leptin receptor binding / sexual reproduction / regulation of natural killer cell mediated cytotoxicity / regulation of bone remodeling / regulation of endothelial cell proliferation / regulation of natural killer cell proliferation / positive regulation of follicle-stimulating hormone secretion / glycerol biosynthetic process / leptin-mediated signaling pathway / ovulation from ovarian follicle / regulation of transport / regulation of brown fat cell differentiation / bone growth / positive regulation of monoatomic ion transport / protein-hormone receptor activity / energy reserve metabolic process / positive regulation of hepatic stellate cell activation / positive regulation of peroxisome proliferator activated receptor signaling pathway / regulation of nitric-oxide synthase activity / regulation of catalytic activity / regulation of feeding behavior / adult feeding behavior / bone mineralization involved in bone maturation / regulation of lipid biosynthetic process / regulation of natural killer cell activation / response to leptin / fatty acid catabolic process / negative regulation of hydrolase activity / negative regulation of D-glucose import across plasma membrane / hormone metabolic process / bile acid metabolic process / negative regulation of appetite / positive regulation of developmental growth / prostaglandin secretion / leukocyte tethering or rolling / aorta development / cellular response to leptin stimulus / cardiac muscle hypertrophy / intestinal absorption / regulation of protein localization to nucleus / positive regulation of p38MAPK cascade / regulation of fat cell differentiation / cell surface receptor signaling pathway via STAT / regulation of gluconeogenesis / cytokine receptor activity / insulin secretion / response to dietary excess / glycogen metabolic process / negative regulation of vasoconstriction / response to vitamin E / eating behavior / fatty acid beta-oxidation / peptide hormone receptor binding / regulation of cytokine production involved in inflammatory response / adipose tissue development / central nervous system neuron development / cytokine binding / regulation of insulin secretion / peptide hormone binding / T cell differentiation / negative regulation of lipid storage / regulation of angiogenesis / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of TOR signaling / cholesterol metabolic process / glial cell proliferation / energy homeostasis / positive regulation of interleukin-12 production / cellular response to retinoic acid / phagocytosis / cell surface receptor signaling pathway via JAK-STAT / determination of adult lifespan / positive regulation of T cell proliferation / placenta development / negative regulation of autophagy / response to activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of interleukin-8 production / lipid metabolic process / positive regulation of receptor signaling pathway via JAK-STAT
Similarity search - Function
Leptin / Leptin receptor, immunoglobulin-like domain / Leptin / 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 receptor, immunoglobulin-like domain / Leptin / 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
NICKEL (II) ION / Leptin / Leptin receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 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 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leptin
B: Leptin receptor
C: Leptin
D: Leptin receptor
E: Leptin
F: Leptin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)349,2349
Polymers349,0586
Non-polymers1763
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, The oligomeric state of the complex was confirmed by SEC-MALLS.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Leptin / Obesity factor


Mass: 18873.283 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-terminally His-tagged mouse leptin was refolded from inclusion bodies produced in E.coli.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lep, Ob / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41160
#2: Protein Leptin receptor / LEP-R / B219 / OB receptor / OB-R


Mass: 97479.391 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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 ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
Has ligand of interestN
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: 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 complex with refolded mouse leptin produced in E.coli.
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 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 solutionpH: 7.4 / Details: 20 mM HEPES, 150 mM NaCl, pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 22 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13230

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARCv3.3.1particle selection
4cryoSPARCv3.3.1CTF correctionPatch ctf
7UCSF Chimera1.17model fitting
9PHENIX1.19.2-4158model refinement
10cryoSPARCv3.3.1initial Euler assignment
11cryoSPARCv3.3.1final Euler assignment
12cryoSPARCv3.3.1classificationAb initio
13cryoSPARCv3.3.13D reconstructionNon-uniform refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 141157
Details: Movies were processed via patch-based motion correction and CTF estimation as implemented in cryoSPARC v3.3.1. Initial 2D classes were obtained by the blob picker function in cryoSPARC, ...Details: Movies were processed via patch-based motion correction and CTF estimation as implemented in cryoSPARC v3.3.1. Initial 2D classes were obtained by the blob picker function in cryoSPARC, followed by particle picking via TOPAZ as implemented in cryoSPARC. Junk particles were removed by multiple rounds of 2D classification and ab initio 3D classification resulting in a particle set of 141,157 particles.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37530 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 275.26 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003517937
ELECTRON MICROSCOPYf_angle_d0.772124447
ELECTRON MICROSCOPYf_chiral_restr0.05242802
ELECTRON MICROSCOPYf_plane_restr0.00523078
ELECTRON MICROSCOPYf_dihedral_angle_d5.3642367

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