+Open data
-Basic information
Entry | Database: PDB / ID: 7xm8 | |||||||||||||||
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Title | Glucagon amyloid fibril | |||||||||||||||
Components | Glucagon | |||||||||||||||
Keywords | PROTEIN FIBRIL / amyloid / fibrils / glucagon | |||||||||||||||
Function / homology | Function and homology information glucagon receptor binding / negative regulation of execution phase of apoptosis / feeding behavior / : / cellular response to glucagon stimulus / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / protein kinase A signaling ...glucagon receptor binding / negative regulation of execution phase of apoptosis / feeding behavior / : / cellular response to glucagon stimulus / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / protein kinase A signaling / positive regulation of gluconeogenesis / response to activity / positive regulation of peptidyl-threonine phosphorylation / gluconeogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / hormone activity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / glucose homeostasis / positive regulation of peptidyl-serine phosphorylation / G alpha (s) signalling events / G alpha (q) signalling events / secretory granule lumen / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||||||||
Authors | Jeong, H. / Lin, Y. / Lee, Y.-H. | |||||||||||||||
Funding support | Korea, Republic Of, 4items
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Citation | Journal: To Be Published Title: Atomistic zipper-like amyloid structure of full-length glucagon Authors: Jeong, H. / Lee, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xm8.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xm8.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/7xm8 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/7xm8 | HTTPS FTP |
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-Related structure data
Related structure data | 33290MC 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/peptide | Mass: 3486.781 Da / Num. of mol.: 22 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01275 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Glucagon amyloid fibril / Type: COMPLEX Details: Glucagon (HSQGTFTSDYSKYLDSRRAQDFVQWLMNT; purity: >97%) was synthesized by Toray Industries (Tokyo, Japan) Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 2.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Glucagon (HSQGTFTSDYSKYLDSRRAQDFVQWLMNT; purity: >97%) was synthesized by Toray Industries (Tokyo, Japan) |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20592 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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