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- EMDB-27433: Leptin-bound leptin receptor complex-D3-D7 -

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Basic information

Entry
Database: EMDB / ID: EMD-27433
TitleLeptin-bound leptin receptor complex-D3-D7
Map dataLeptin-bound leptin receptor complex-D3-D7
Sample
  • Complex: Leptin Receptor Complex
    • Protein or peptide: Leptin receptor
    • Protein or peptide: Leptin
Keywordsleptin / receptor / complex / HORMONE
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 / regulation of bone remodeling / positive regulation of luteinizing hormone secretion / bone growth / regulation of natural killer cell activation / glycerol biosynthetic process / regulation of steroid biosynthetic process / elastin metabolic process / leptin-mediated signaling pathway / positive regulation of follicle-stimulating hormone secretion / positive regulation of monoatomic ion transport / regulation of intestinal cholesterol absorption / positive regulation of hepatic stellate cell activation / regulation of brown fat cell differentiation / positive regulation of peroxisome proliferator activated receptor signaling pathway / regulation of nitric-oxide synthase activity / adult feeding behavior / activation of protein kinase C activity / bone mineralization involved in bone maturation / regulation of lipid biosynthetic process / response to leptin / regulation of feeding behavior / sexual reproduction / negative regulation of cartilage development / ovulation from ovarian follicle / negative regulation of D-glucose import / negative regulation of appetite / positive regulation of developmental growth / energy reserve metabolic process / leukocyte tethering or rolling / bile acid metabolic process / cellular response to leptin stimulus / prostaglandin secretion / cardiac muscle hypertrophy / regulation of protein localization to nucleus / hormone metabolic process / intestinal absorption / positive regulation of p38MAPK cascade / regulation of fat cell differentiation / insulin secretion / regulation of metabolic process / eating behavior / aorta development / negative regulation of vasoconstriction / regulation of gluconeogenesis / response to vitamin E / glycogen metabolic process / peptide hormone receptor binding / 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 / positive regulation of TOR signaling / regulation of angiogenesis / cell surface receptor signaling pathway via JAK-STAT / positive regulation of insulin receptor signaling pathway / adipose tissue development / negative regulation of gluconeogenesis / phagocytosis / glial cell proliferation / energy homeostasis / cellular response to retinoic acid / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / negative regulation of autophagy / regulation of insulin secretion / cholesterol metabolic process / female pregnancy / placenta development / response to activity / gluconeogenesis / positive regulation of interleukin-8 production / determination of adult lifespan / positive regulation of receptor signaling pathway via JAK-STAT / response to insulin / hormone activity / regulation of blood pressure / positive regulation of interleukin-6 production / lipid metabolic process / positive regulation of protein import into nucleus / circadian rhythm / cellular response to insulin stimulus / glucose metabolic process / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsSaxton RA / Caveney NA / Garcia KC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into the mechanism of leptin receptor activation.
Authors: Robert A Saxton / Nathanael A Caveney / Maria Dolores Moya-Garzon / Karsten D Householder / Grayson E Rodriguez / Kylie A Burdsall / Jonathan Z Long / K Christopher Garcia /
Abstract: Leptin is an adipocyte-derived protein hormone that promotes satiety and energy homeostasis by activating the leptin receptor (LepR)-STAT3 signaling axis in a subset of hypothalamic neurons. Leptin ...Leptin is an adipocyte-derived protein hormone that promotes satiety and energy homeostasis by activating the leptin receptor (LepR)-STAT3 signaling axis in a subset of hypothalamic neurons. Leptin signaling is dysregulated in obesity, however, where appetite remains elevated despite high levels of circulating leptin. To gain insight into the mechanism of leptin receptor activation, here we determine the structure of a stabilized leptin-bound LepR signaling complex using single particle cryo-EM. The structure reveals an asymmetric architecture in which a single leptin induces LepR dimerization via two distinct receptor-binding sites. Analysis of the leptin-LepR binding interfaces reveals the molecular basis for human obesity-associated mutations. Structure-based design of leptin variants that destabilize the asymmetric LepR dimer yield both partial and biased agonists that partially suppress STAT3 activation in the presence of wild-type leptin and decouple activation of STAT3 from LepR negative regulators. Together, these results reveal the structural basis for LepR activation and provide insights into the differential plasticity of signaling pathways downstream of LepR.
History
DepositionJun 25, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27433.png

Downloads & links

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Map

FileDownload / File: emd_27433.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLeptin-bound leptin receptor complex-D3-D7
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 320 pix.
= 381.741 Å		1.19 Å/pix.
x 320 pix.
= 381.741 Å		1.19 Å/pix.
x 320 pix.
= 381.741 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.059399087 - 1.8096325
Average (Standard dev.)0.0003414304 (±0.013903098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 381.74078 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27433_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Half map: Leptin-bound leptin receptor complex-D3-D7

Fileemd_27433_half_map_1.map
AnnotationLeptin-bound leptin receptor complex-D3-D7
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Leptin-bound leptin receptor complex-D3-D7

Fileemd_27433_half_map_2.map
AnnotationLeptin-bound leptin receptor complex-D3-D7
Projections & Slices
AxesZYX

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Sample components

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Entire : Leptin Receptor Complex

EntireName: Leptin Receptor Complex
Components
  • Complex: Leptin Receptor Complex
    • Protein or peptide: Leptin receptor
    • Protein or peptide: Leptin

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Supramolecule #1: Leptin Receptor Complex

SupramoleculeName: Leptin Receptor Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Leptin receptor

MacromoleculeName: Leptin receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 63.674754 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TQDVVYFPPK ILTSVGSNAS FHCIYKNENQ IISSKQIVWW RNLAEKIPEI QYSIVSDRVS KVTFSNLKAT RPRGKFTYDA VYCCNEQAC HHRYAELYVI DVNINISCET DGYLTKMTCR WSPSTIQSLV GSTVQLRYHR RSLYCPDSPS IHPTSEPKNC V LQRDGFYE ...String:
TQDVVYFPPK ILTSVGSNAS FHCIYKNENQ IISSKQIVWW RNLAEKIPEI QYSIVSDRVS KVTFSNLKAT RPRGKFTYDA VYCCNEQAC HHRYAELYVI DVNINISCET DGYLTKMTCR WSPSTIQSLV GSTVQLRYHR RSLYCPDSPS IHPTSEPKNC V LQRDGFYE CVFQPIFLLS GYTMWIRINH SLGSLDSPPT CVLPDSVVKP LPPSNVKAEI TVNTGLLKVS WEKPVFPENN LQ FQIRYGL SGKEIQWKTH EVFDAKSKSA SLLVSDLCAV YVVQVRCRRL DGLGYWSNWS SPAYTLVMDV KVPMRGPEFW RKM DGDVTK KERNVTLLWK PLTKNDSLCS VRRYVVKHRT AHNGTWSEDV GNRTNLTFLW TEPAHTVTVL AVNSLGASLV NFNL TFSWP MSKVSAVESL SAYPLSSSCV ILSWTLSPDD YSLLYLVIEW KILNEDDGMK WLRIPSNVKK FYIHDNFIPI EKYQF SLYP VFMEGVGKPK IINGFTKDAI DKQQNDAGGS GGMKQLEDKV EELLSKNYHL ENEVARLKKL VGERSGGHHH HHH

UniProtKB: Leptin receptor

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Macromolecule #2: Leptin

MacromoleculeName: Leptin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.724555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MCWRPLCRFL WLWSYLSYVQ AVPIQKVQDD TKTLIKTIVT RINDISHTQS VSAKQRVTGL DFIPGLHPIL SLSKMDQTLA VYQQVLTSL PSQNVLQIAN DLENLRDLLH LLAFSKSCSL PQTSGLQKPE SLDGVLEASL YSTEVVALSR LQGSLQDILQ Q LDVSPEC

UniProtKB: Leptin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137338
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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