[English] 日本語
Yorodumi
- EMDB-33290: Glucagon amyloid fibril -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / cellular response to glucagon stimulus / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis ...glucagon receptor binding / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / cellular response to glucagon stimulus / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / protein kinase A signaling / positive regulation of peptidyl-threonine phosphorylation / response to activity / gluconeogenesis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / 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 / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis / 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
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 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33290.png

Downloads & links

-
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 °

-
Supplemental data

-
Additional map: refined

Fileemd_33290_additional_1.map
Annotationrefined
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half1

Fileemd_33290_half_map_1.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2

Fileemd_33290_half_map_2.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Glucagon amyloid fibril

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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
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)

-
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

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more