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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 / regulation of natural killer cell mediated cytotoxicity / leptin receptor binding ...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 / regulation of natural killer cell mediated cytotoxicity / 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 / sexual reproduction / negative regulation of cartilage development / negative regulation of D-glucose import across plasma membrane / negative regulation of appetite / ovulation from ovarian follicle / positive regulation of developmental growth / energy reserve metabolic process / leukocyte tethering or rolling / cellular response to leptin stimulus / bile acid metabolic process / prostaglandin secretion / cardiac muscle hypertrophy / Signaling by Leptin / hormone metabolic process / positive regulation of p38MAPK cascade / cell surface receptor signaling pathway via STAT / intestinal absorption / eating behavior / insulin secretion / aorta development / regulation of gluconeogenesis / negative regulation of vasoconstriction / response to vitamin E / 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 / T cell differentiation / negative regulation of lipid storage / Synthesis, secretion, and deacylation of Ghrelin / regulation of angiogenesis / positive regulation of TOR signaling / cell surface receptor signaling pathway via JAK-STAT / adipose tissue development / positive regulation of insulin receptor signaling pathway / phagocytosis / cholesterol metabolic process / energy homeostasis / 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 / determination of adult lifespan / positive regulation of interleukin-8 production / 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 interleukin-6 production / positive regulation of protein import into nucleus / lipid metabolic process / regulation of blood pressure / cellular response to insulin stimulus / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / positive regulation of tumor necrosis factor production / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / response to estradiol / glucose homeostasis / positive regulation of cold-induced thermogenesis / response to ethanol / angiogenesis / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell cycle / positive regulation of MAPK cascade
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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Has protein modificationY

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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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