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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


regulation of transport / 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 / negative regulation of appetite by leptin-mediated signaling pathway / negative regulation of glucagon secretion / regulation of endothelial cell proliferation ...regulation of transport / 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 / negative regulation of appetite by leptin-mediated signaling pathway / negative regulation of glucagon secretion / regulation of endothelial cell proliferation / regulation of natural killer cell proliferation / leptin receptor binding / regulation of natural killer cell mediated cytotoxicity / bone growth / positive regulation of luteinizing hormone secretion / regulation of natural killer cell activation / glycerol biosynthetic process / positive regulation of monoatomic ion transport / elastin metabolic process / leptin-mediated signaling pathway / positive regulation of follicle-stimulating hormone secretion / regulation of steroid biosynthetic process / regulation of intestinal cholesterol absorption / regulation of bone remodeling / regulation of brown fat cell differentiation / positive regulation of peroxisome proliferator activated receptor signaling pathway / positive regulation of hepatic stellate cell activation / adult feeding behavior / regulation of nitric-oxide synthase activity / response to leptin / bone mineralization involved in bone maturation / sexual reproduction / regulation of feeding behavior / activation of protein kinase C activity / negative regulation of cartilage development / 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 / negative regulation of D-glucose import / cellular response to leptin stimulus / prostaglandin secretion / cardiac muscle hypertrophy / hormone metabolic process / Signaling by Leptin / aorta development / intestinal absorption / insulin secretion / cytokine receptor activity / positive regulation of p38MAPK cascade / negative regulation of vasoconstriction / eating behavior / peptide hormone receptor binding / regulation of gluconeogenesis / glycogen metabolic process / fatty acid beta-oxidation / regulation of cytokine production involved in inflammatory response / central nervous system neuron development / cytokine binding / response to dietary excess / negative regulation of lipid storage / T cell differentiation / transport across blood-brain barrier / positive regulation of TOR signaling / Synthesis, secretion, and deacylation of Ghrelin / response to vitamin E / glial cell proliferation / negative regulation of gluconeogenesis / adipose tissue development / regulation of angiogenesis / phagocytosis / positive regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / energy homeostasis / cellular response to retinoic acid / positive regulation of interleukin-12 production / regulation of insulin secretion / cholesterol metabolic process / negative regulation of autophagy / response to activity / gluconeogenesis / positive regulation of interleukin-8 production / female pregnancy / determination of adult lifespan / positive regulation of receptor signaling pathway via JAK-STAT / response to insulin / placenta development / lipid metabolic process / hormone activity / cytokine-mediated signaling pathway / Transcriptional regulation of white adipocyte differentiation / regulation of blood pressure / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / circadian rhythm / 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. / : ...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-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38131.png

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)
Projections & slices

Image control

Size
Brightness
Contrast
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-0.0017401059 - 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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Half map: #1

Fileemd_38131_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38131_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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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

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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