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- EMDB-38131: Structure of leptin-LepR trimer with a small gap -

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Basic information

Entry
Database: EMDB / ID: EMD-38131
TitleStructure of leptin-LepR trimer with a small gap
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 / hexamer / CYTOKINE
Function / homology
Function and homology information


multicellular organism development / 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 / negative regulation of glucagon secretion / regulation of endothelial cell proliferation ...multicellular organism development / 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 / 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 feeding behavior / 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 / sexual reproduction / response to leptin / negative regulation of cartilage development / ovulation from ovarian follicle / negative regulation of D-glucose import / 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 / prostaglandin secretion / cardiac muscle hypertrophy / Signaling by Leptin / hormone metabolic process / positive regulation of p38MAPK cascade / cell surface receptor signaling pathway via STAT / cytokine receptor activity / intestinal absorption / insulin secretion / 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 / cytokine binding / central nervous system neuron development / response to dietary excess / energy homeostasis / peptide hormone binding / negative regulation of lipid storage / T cell differentiation / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of TOR signaling / cell surface receptor signaling pathway via JAK-STAT / regulation of angiogenesis / positive regulation of insulin receptor signaling pathway / negative regulation of gluconeogenesis / adipose tissue development / phagocytosis / glial cell proliferation / transport across blood-brain barrier / cholesterol metabolic process / cellular response to retinoic acid / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / regulation of insulin secretion / negative regulation of autophagy / placenta development / response to activity / gluconeogenesis / determination of adult lifespan / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / female pregnancy / response to insulin / circadian rhythm / hormone activity / Transcriptional regulation of white adipocyte differentiation / lipid metabolic process / regulation of blood pressure / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / cellular response to insulin stimulus
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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsXie YF / 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

Downloads & links

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Map

FileDownload / File: emd_38131.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.0017401059 - 2.196138
Average (Standard dev.)0.0005532392 (±0.015951669)
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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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: 3 / 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: 3 / 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: 15 / 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: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103388
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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