+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38132 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of leptin-LepR trimer with a large gap | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | cytokine receptor / hexamer / CYTOKINE | |||||||||
Function / homology | Function and homology information regulation of transport / 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 ...regulation of transport / 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 / 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 / positive regulation of hepatic stellate cell activation / response to leptin / adult feeding behavior / regulation of nitric-oxide synthase activity / bone mineralization involved in bone maturation / sexual reproduction / regulation of feeding behavior / activation of protein kinase C activity / negative regulation of cartilage development / multicellular organism 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 / cardiac muscle hypertrophy / hormone metabolic process / Signaling by Leptin / aorta development / insulin secretion / intestinal absorption / positive regulation of p38MAPK cascade / peptide hormone receptor binding / cytokine receptor activity / negative regulation of vasoconstriction / eating behavior / regulation of gluconeogenesis / glycogen metabolic process / fatty acid beta-oxidation / central nervous system neuron development / cytokine binding / regulation of cytokine production involved in inflammatory response / regulation of insulin secretion / response to dietary excess / negative regulation of lipid storage / transport across blood-brain barrier / T cell differentiation / positive regulation of TOR signaling / response to vitamin E / Synthesis, secretion, and deacylation of Ghrelin / glial cell proliferation / regulation of angiogenesis / adipose tissue development / negative regulation of gluconeogenesis / phagocytosis / energy homeostasis / positive regulation of insulin receptor signaling pathway / cellular response to retinoic acid / 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 / gluconeogenesis / 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 / cytokine-mediated signaling pathway / 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 / transmembrane signaling receptor activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.77 Å | |||||||||
Authors | Xie YF / Gao GF | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_38132.map.gz | 532.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-38132-v30.xml emd-38132.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_38132.png | 54.2 KB | ||
Filedesc metadata | emd-38132.cif.gz | 5.9 KB | ||
Others | emd_38132_half_map_1.map.gz emd_38132_half_map_2.map.gz | 558.2 MB 558.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38132 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38132 | HTTPS FTP |
-Validation report
Summary document | emd_38132_validation.pdf.gz | 685.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_38132_full_validation.pdf.gz | 684.8 KB | Display | |
Data in XML | emd_38132_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | emd_38132_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38132 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38132 | HTTPS FTP |
-Related structure data
Related structure data | 8x81MC 8x80C 8x85C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_38132.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #1
File | emd_38132_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_38132_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Leptin-LepR complex
Entire | Name: Leptin-LepR complex |
---|---|
Components |
|
-Supramolecule #1: Leptin-LepR complex
Supramolecule | Name: Leptin-LepR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Leptin receptor
Macromolecule | Name: Leptin receptor / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 94.93357 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Leptin
Macromolecule | Name: Leptin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.6565 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MHWGTLCGFL WLWPYLFYVQ AVPIQKVQDD TKTLIKTIVT RINDISHTQS VSSKQKVTGL DFIPGLHPIL TLSKMDQTLA VYQQILTSM PSRNVIQISN DLENLRDLLH VLAFSKSCHL PWASGLETLD SLGGVLEASG YSTEVVALSR LQGSLQDMLW Q LDLSPGC UniProtKB: Leptin |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 19 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: INSILICO MODEL |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106339 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |