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- EMDB-38136: Structure of leptin-LepR dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-38136
TitleStructure of leptin-LepR dimer
Map data
Sample
  • Complex: Leptin-LepR complex
    • Protein or peptide: Leptin receptor
    • Protein or peptide: Leptin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscytokine receptor / tetramer / CYTOKINE
Function / homology
Function and homology information


multicellular organism development / 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 / positive regulation of luteinizing hormone secretion / negative regulation of glucagon secretion ...multicellular organism development / 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 / positive regulation of luteinizing hormone secretion / negative regulation of glucagon secretion / negative regulation of cartilage development / 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 / 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 feeding behavior / adult feeding behavior / bone mineralization involved in bone maturation / regulation of natural killer cell activation / response to leptin / fatty acid catabolic process / negative regulation of D-glucose import across plasma membrane / negative regulation of appetite / positive regulation of developmental growth / prostaglandin secretion / leukocyte tethering or rolling / cellular response to leptin stimulus / cardiac muscle hypertrophy / intestinal absorption / Signaling by Leptin / positive regulation of p38MAPK cascade / cell surface receptor signaling pathway via STAT / cytokine receptor activity / response to dietary excess / negative regulation of vasoconstriction / response to vitamin E / peptide hormone receptor binding / regulation of cytokine production involved in inflammatory response / cytokine binding / peptide hormone binding / T cell differentiation / negative regulation of lipid storage / Synthesis, secretion, and deacylation of Ghrelin / regulation of angiogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of TOR signaling / energy homeostasis / positive regulation of interleukin-12 production / cellular response to retinoic acid / phagocytosis / cell surface receptor signaling pathway via JAK-STAT / transport across blood-brain barrier / positive regulation of T cell proliferation / placenta development / negative regulation of autophagy / response to activity / positive regulation of interleukin-8 production / lipid metabolic process / positive regulation of receptor signaling pathway via JAK-STAT / female pregnancy / circadian rhythm / response to insulin / hormone activity / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / regulation of blood pressure / positive regulation of reactive oxygen species metabolic process / cytokine-mediated signaling pathway / glucose homeostasis / positive regulation of tumor necrosis factor production / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / response to estradiol / transmembrane signaling receptor activity / positive regulation of cold-induced thermogenesis / angiogenesis / response to ethanol / basolateral plasma membrane / response to hypoxia / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell cycle / signaling receptor complex / cell surface receptor signaling pathway / intracellular signal transduction / external side of plasma membrane
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
Leptin / Leptin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsXie YF / Shang GJ / Qi JX / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Hlife / Year: 2023
Title: Structural plasticity of human leptin binding to its receptor LepR
Authors: Xie YF / Li X / Qi J / Shang G / Lu D / Gao GF
History
DepositionNov 27, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38136.png

Downloads & links

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Map

FileDownload / File: emd_38136.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 540 pix.
= 459. Å		0.85 Å/pix.
x 540 pix.
= 459. Å		0.85 Å/pix.
x 540 pix.
= 459. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.001749627 - 2.0361946
Average (Standard dev.)0.00030152404 (±0.01234409)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 459.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38136_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_38136_half_map_2.map
Projections & Slices
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Sample components

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Entire : Leptin-LepR complex

EntireName: Leptin-LepR complex
Components
  • Complex: Leptin-LepR complex
    • Protein or peptide: Leptin receptor
    • Protein or peptide: Leptin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Leptin-LepR complex

SupramoleculeName: Leptin-LepR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 94.93357 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AFNLSYPITP WRFKLSCMPP NSTYDYFLLP AGLSKNTSNS NGHYETAVEP KFNSSGTHFS NLSKTTFHCC FRSEQDRNCS LCADNIEGK TFVSTVNSLV FQQIDANWNI QCWLKGDLKL FICYVESLFK NLFRNYNYKV HLLYVLPEVL EDSPLVPQKG S FQMVHCNC ...String:
AFNLSYPITP WRFKLSCMPP NSTYDYFLLP AGLSKNTSNS NGHYETAVEP KFNSSGTHFS NLSKTTFHCC FRSEQDRNCS LCADNIEGK TFVSTVNSLV FQQIDANWNI QCWLKGDLKL FICYVESLFK NLFRNYNYKV HLLYVLPEVL EDSPLVPQKG S FQMVHCNC SVHECCECLV PVPTAKLNDT LLMCLKITSG GVIFQSPLMS VQPINMVKPD PPLGLHMEIT DDGNLKISWS SP PLVPFPL QYQVKYSENS TTVIREADKI VSATSLLVDS ILPGSSYEVQ VRGKRLDGPG IWSDWSTPRV FTTQDVIYFP PKI LTSVGS NVSFHCIYKK ENKIVPSKEI VWWMNLAEKI PQSQYDVVSD HVSKVTFFNL NETKPRGKFT YDAVYCCNEH ECHH RYAEL YVIDVNINIS CETDGYLTKM TCRWSTSTIQ SLAESTLQLR YHRSSLYCSD IPSIHPISEP KDCYLQSDGF YECIF QPIF LLSGYTMWIR INHSLGSLDS PPTCVLPDSV VKPLPPSSVK AEITINIGLL KISWEKPVFP ENNLQFQIRY GLSGKE VQW KMYEVYDAKS KSVSLPVPDL CAVYAVQVRC KRLDGLGYWS NWSNPAYTVV MDIKVPMRGP EFWRIINGDT MKKEKNV TL LWKPLMKNDS LCSVQRYVIN HHTSCNGTWS EDVGNHTKFT FLWTEQAHTV TVLAINSIGA SVANFNLTFS WPMSKVNI V QSLSAYPLNS SCVIVSWILS PSDYKLMYFI IEWKNLNEDG EIKWLRISSS VKKYYIHDHF IPIEKYQFSL YPIFMEGVG KPKIINSFTQ DDIEKHQSDG THHHHHHHH

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: Homo sapiens (human)
Molecular weightTheoretical: 18.6565 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MHWGTLCGFL WLWPYLFYVQ AVPIQKVQDD TKTLIKTIVT RINDISHTQS VSSKQKVTGL DFIPGLHPIL TLSKMDQTLA VYQQILTSM PSRNVIQISN DLENLRDLLH VLAFSKSCHL PWASGLETLD SLGGVLEASG YSTEVVALSR LQGSLQDMLW Q LDLSPGC

UniProtKB: Leptin

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 11 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115281
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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