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- PDB-7xm8: Glucagon amyloid fibril -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7xm8
TitleGlucagon amyloid fibril
ComponentsGlucagon
KeywordsPROTEIN FIBRIL / amyloid / fibrils / glucagon
Function / homology
Function and homology information


glucagon receptor binding / : / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of gluconeogenesis / cellular response to glucagon stimulus / regulation of insulin secretion ...glucagon receptor binding / : / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of gluconeogenesis / cellular response to glucagon stimulus / regulation of insulin secretion / response to activity / gluconeogenesis / hormone activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / 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 / secretory granule lumen / G alpha (s) signalling events / G alpha (q) signalling events / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Glucagon / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJeong, H. / Lin, Y. / Lee, Y.-H.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2022R1A2C1011793 Korea, Republic Of
Other governmentC220000 Korea, Republic Of
Other governmentC230130 Korea, Republic Of
Other governmentC280300 Korea, Republic Of
CitationJournal: To Be Published
Title: Atomistic zipper-like amyloid structure of full-length glucagon
Authors: Jeong, H. / Lee, Y.
History
DepositionApr 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.0Apr 19, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Glucagon
G: Glucagon
J: Glucagon
I: Glucagon
K: Glucagon
F: Glucagon
B: Glucagon
A: Glucagon
D: Glucagon
C: Glucagon
E: Glucagon
T: Glucagon
S: Glucagon
V: Glucagon
U: Glucagon
R: Glucagon
N: Glucagon
M: Glucagon
P: Glucagon
O: Glucagon
Q: Glucagon
L: Glucagon


Theoretical massNumber of molelcules
Total (without water)76,70922
Polymers76,70922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
Glucagon


Mass: 3486.781 Da / Num. of mol.: 22 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01275
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Glucagon amyloid fibril / Type: COMPLEX
Details: Glucagon (HSQGTFTSDYSKYLDSRRAQDFVQWLMNT; purity: >97%) was synthesized by Toray Industries (Tokyo, Japan)
Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 2.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Glucagon (HSQGTFTSDYSKYLDSRRAQDFVQWLMNT; purity: >97%) was synthesized by Toray Industries (Tokyo, Japan)
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20592 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0125544
ELECTRON MICROSCOPYf_angle_d1.5017480
ELECTRON MICROSCOPYf_dihedral_angle_d16.0991958
ELECTRON MICROSCOPYf_chiral_restr0.12748
ELECTRON MICROSCOPYf_plane_restr0.005968

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