+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38131 | |||||||||
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Title | Structure of leptin-LepR trimer with a small gap | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cytokine receptor / hexamer / CYTOKINE | |||||||||
Function / homology | Function and homology information leptin receptor activity / regulation of transport / bone growth / leptin-mediated signaling pathway / regulation of bone remodeling / response to leptin / regulation of feeding behavior / sexual reproduction / multicellular organism development / energy reserve metabolic process ...leptin receptor activity / regulation of transport / bone growth / leptin-mediated signaling pathway / regulation of bone remodeling / response to leptin / regulation of feeding behavior / sexual reproduction / multicellular organism development / energy reserve metabolic process / Signaling by Leptin / cytokine receptor activity / glycogen metabolic process / cytokine binding / transport across blood-brain barrier / T cell differentiation / glial cell proliferation / negative regulation of gluconeogenesis / phagocytosis / energy homeostasis / cholesterol metabolic process / negative regulation of autophagy / gluconeogenesis / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / positive regulation of cold-induced thermogenesis / glucose homeostasis / basolateral plasma membrane / angiogenesis / receptor complex / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / external side of plasma membrane / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.88 Å | |||||||||
Authors | Xie YF / Gao GF | |||||||||
Funding support | China, 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38131.map.gz | 532.5 MB | EMDB map data format | |
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Header (meta data) | emd-38131-v30.xml emd-38131.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_38131.png | 50.1 KB | ||
Filedesc metadata | emd-38131.cif.gz | 6 KB | ||
Others | emd_38131_half_map_1.map.gz emd_38131_half_map_2.map.gz | 558.3 MB 558.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38131 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38131 | HTTPS FTP |
-Validation report
Summary document | emd_38131_validation.pdf.gz | 677.7 KB | Display | EMDB validaton report |
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Full document | emd_38131_full_validation.pdf.gz | 677.3 KB | Display | |
Data in XML | emd_38131_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | emd_38131_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38131 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38131 | HTTPS FTP |
-Related structure data
Related structure data | 8x80MC 8x81C 8x85C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38131.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_38131_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38131_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Leptin-LepR complex
Entire | Name: Leptin-LepR complex |
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Components |
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-Supramolecule #1: Leptin-LepR complex
Supramolecule | Name: Leptin-LepR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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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 |
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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 |
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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: UNIPROTKB: P41159 |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103388 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |