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- PDB-8k6z: NMR structure of human leptin -

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Basic information

Entry
Database: PDB / ID: 8k6z
TitleNMR structure of human leptin
ComponentsLeptin
KeywordsCYTOKINE / helical / energy homeostasis
Function / homology
Function and homology information


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 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 / positive regulation of luteinizing hormone secretion ...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 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 / positive regulation of luteinizing hormone secretion / regulation of natural killer cell mediated cytotoxicity / bone growth / regulation of natural killer cell activation / positive regulation of monoatomic ion transport / glycerol biosynthetic process / 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 / adult feeding behavior / positive regulation of hepatic stellate cell activation / regulation of nitric-oxide synthase activity / bone mineralization involved in bone maturation / sexual reproduction / 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 / negative regulation of glucose import / prostaglandin secretion / bile acid metabolic process / cellular response to leptin stimulus / hormone metabolic process / cardiac muscle hypertrophy / Signaling by Leptin / aorta development / intestinal absorption / insulin secretion / positive regulation of p38MAPK cascade / peptide hormone receptor binding / negative regulation of vasoconstriction / eating behavior / regulation of gluconeogenesis / fatty acid beta-oxidation / central nervous system neuron development / regulation of cytokine production involved in inflammatory response / regulation of insulin secretion / response to dietary excess / negative regulation of lipid storage / T cell differentiation / positive regulation of TOR signaling / Synthesis, secretion, and deacylation of Ghrelin / response to vitamin E / regulation of angiogenesis / adipose tissue development / phagocytosis / cellular response to retinoic acid / positive regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-12 production / cholesterol metabolic process / negative regulation of autophagy / response to activity / positive regulation of interleukin-8 production / determination of adult lifespan / female pregnancy / positive regulation of receptor signaling pathway via JAK-STAT / response to insulin / placenta development / hormone activity / lipid metabolic process / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein import into nucleus / circadian rhythm / cellular response to insulin stimulus / glucose metabolic process / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of reactive oxygen species metabolic process / response to estradiol / glucose homeostasis / positive regulation of cold-induced thermogenesis / angiogenesis / response to ethanol / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / regulation of cell cycle / intracellular signal transduction / positive regulation of protein phosphorylation
Similarity search - Function
Leptin / Leptin / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsFan, X. / Qin, R. / Yuan, W. / Fan, J. / Huang, W. / Lin, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22274111 China
CitationJournal: Structure / Year: 2024
Title: The solution structure of human leptin reveals a conformational plasticity important for receptor recognition.
Authors: Fan, X. / Qin, R. / Yuan, W. / Fan, J.S. / Huang, W. / Lin, Z.
History
DepositionJul 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leptin


Theoretical massNumber of molelcules
Total (without water)16,0411
Polymers16,0411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Leptin / Obese protein / Obesity factor


Mass: 16041.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LEP, OB, OBS / Production host: Escherichia coli (E. coli) / References: UniProt: P41159

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aromatic
131isotropic12D 1H-13C HSQC aliphatic
141isotropic13D HNCA
151isotropic13D HN(CO)CA
161isotropic13D (H)CCH-TOCSY
171isotropic14D time-shared 13C, 15N-edited NOESY

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Sample preparation

DetailsType: solution / Contents: 0.8 mM [U-13C; U-15N] leptin, 95% H2O/5% D2O / Label: 15N/13C_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.8 mM / Component: leptin / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 5 mM / Label: 15N/13C / pH: 4.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: distance geometry / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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