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- EMDB-33290: Glucagon amyloid fibril -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33290
TitleGlucagon amyloid fibril
Map datapostprocess_masked
Sample
  • Complex: Glucagon amyloid fibril
    • Protein or peptide: Glucagon
Keywordsamyloid / fibrils / glucagon / PROTEIN FIBRIL
Function / homology
Function and homology information


glucagon receptor binding / protein kinase A signaling / 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 / protein kinase A signaling / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJeong H / Lin Y / Lee Y-H
Funding support Korea, Republic Of, 4 items
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, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_33290.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocess_masked
Voxel sizeX=Y=Z: 0.865 Å
Density
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.10147108 - 0.13687102
Average (Standard dev.)0.0020197711 (±0.0130780805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 103.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Glucagon amyloid fibril

EntireName: Glucagon amyloid fibril
Components
  • Complex: Glucagon amyloid fibril
    • Protein or peptide: Glucagon

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Supramolecule #1: Glucagon amyloid fibril

SupramoleculeName: Glucagon amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Glucagon (HSQGTFTSDYSKYLDSRRAQDFVQWLMNT; purity: >97%) was synthesized by Toray Industries (Tokyo, Japan)
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glucagon

MacromoleculeName: Glucagon / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.486781 KDa
SequenceString:
HSQGTFTSDY SKYLDSRRAQ DFVQWLMNT

UniProtKB: Pro-glucagon

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 2.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE
DetailsGlucagon (HSQGTFTSDYSKYLDSRRAQDFVQWLMNT; purity: >97%) was synthesized by Toray Industries (Tokyo, Japan)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20592
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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