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Autophagy01:27

Autophagy

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Autophagy is a self-digesting process by which a cell protects itself from threats both within and outside the cell, ranging from abnormal proteins to invading bacteria. In this process, obsolete components of the cell and invading microbes are degraded by hydrolytic enzymes active in an acidic environment of the lysosomal lumen.
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Eukaryotic cells use different mechanisms to eliminate toxic waste obsolete and worn-out substances. Lysosomes play a pivotal role in this, and hence, these substances are carried to the lysosome from other parts of the cell and extracellular space through different pathways. The most elaborately studied pathways to the lysosome are the endocytic pathways.
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Christian de Duve discovered “autophagy,” a process in which cellular components are engulfed by membrane-bound organelles called autophagosomes. The autophagosomes then fuse with lysosomes to digest the enclosed contents. Autophagy is generally activated in cells to prevent cell death. However, cell death is triggered when the damage is beyond repair.
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The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
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Lysosomal Hydrolases01:22

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Lysosomes are the site for the degradation of macromolecules and biological polymers released during membrane trafficking events such as secretory, endocytic, autophagic, and phagocytic pathways. The membrane-enclosed area of the lysosome, called the lumen, contains hydrolytic enzymes active in an acidic environment. These acid hydrolases are functional at a pH between 4.5 and 5 and are involved in cellular processes such as cell signaling, energy metabolism, restoration of the plasma membrane,...
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Updated: Jun 12, 2025

Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy
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Autophagy3D: a comprehensive autophagy structure database.

Neha1, Jesu Castin1, Saman Fatihi1,2

  • 1Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India.

Database : the Journal of Biological Databases and Curation
|September 19, 2024
PubMed
Summary
This summary is machine-generated.

Autophagy3D provides a new web resource for 40 core human autophagic proteins and their interactors. This database enhances access to protein structures, aiding biological insights into cellular degradation.

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Area of Science:

  • Structural biology
  • Cellular biology
  • Bioinformatics

Background:

  • The autophagy pathway is crucial for cellular degradation but studying its core proteins has been limited due to their localization.
  • Advances in cryo-electron microscopy (cryo-EM) and AI-driven protein structure prediction (AlphaFold2) have revolutionized structural biology.

Purpose of the Study:

  • To develop Autophagy3D, a comprehensive web-based database for core human autophagic proteins.
  • To provide easy access to protein structures, interactors, and orthologs, facilitating biological insights.

Main Methods:

  • Development of a web-based resource, Autophagy3D.
  • Integration of structural data for 40 core human autophagic proteins (80,322 structures).
  • Inclusion of protein-protein interactors and ortholog structures from diverse species.

Main Results:

  • Autophagy3D offers detailed visualizations of protein structures.
  • The database provides access to 80,322 structures of core human autophagic proteins and their related interactors/orthologs.
  • Full datasets are available for download, significantly enhancing information accessibility.

Conclusions:

  • Autophagy3D serves as a valuable, publicly accessible resource for researchers studying the autophagy pathway.
  • The database streamlines access to structural information, promoting deeper understanding of cellular degradation mechanisms.