+Open data
-Basic information
Entry | Database: PDB / ID: 8x80 | ||||||
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Title | Structure of leptin-LepR trimer with a small gap | ||||||
Components |
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Keywords | CYTOKINE / cytokine receptor / hexamer | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å | ||||||
Authors | Xie, Y.F. / Gao, G.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Hlife / Year: 2023 Title: Structural plasticity of human leptin binding to its receptor LepR Authors: Xie, Y.F. / Li, X. / Qi, J. / Shang, G. / Lu, D. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8x80.cif.gz | 485.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x80.ent.gz | 398.5 KB | Display | PDB format |
PDBx/mmJSON format | 8x80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x80_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8x80_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8x80_validation.xml.gz | 91.1 KB | Display | |
Data in CIF | 8x80_validation.cif.gz | 132.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/8x80 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/8x80 | HTTPS FTP |
-Related structure data
Related structure data | 38131MC 8x81C 8x85C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 94933.570 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LEPR, DB, OBR / Production host: Homo sapiens (human) / References: UniProt: P48357 #2: Protein | Mass: 18656.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LEP / Production host: Homo sapiens (human) / References: UniProt: P41159 #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Leptin-LepR complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103388 / Symmetry type: POINT |