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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Monitoring carbohydrate 3D structure quality with the Privateer database.

Jordan S Dialpuri1, Haroldas Bagdonas1, Lucy C Schofield1

  • 1York Structural Biology Laboratory, Department of Chemistry, University of York, UK.

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|May 7, 2024
PubMed
Summary
This summary is machine-generated.

The Protein Data Bank (PDB) now has better carbohydrate data, but quality indicators are missing. The new Privateer database offers validation tools to help scientists accurately assess glycan structures.

Keywords:
N-glycansN-glycosylationcarbohydratesdatabasepolysaccharidesvalidationwebsite

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Chemistry

Background:

  • The Protein Data Bank (PDB) has improved glycan structure data, but lacks essential quality indicators.
  • Inexperienced scientists may misinterpret flawed glycan structures due to missing quality metrics on PDB pages.
  • Access to broader glycochemical context is limited, hindering accurate structure evaluation.

Purpose of the Study:

  • To introduce the Privateer database as a free resource for evaluating glycan structures.
  • To complement the PDB's glycan data with crucial quality indicators and validation tools.
  • To aid scientists in assessing the reliability of deposited carbohydrate structures.

Main Methods:

  • Utilizing the Privateer software, a validation and analysis tool for glycan structures.
  • Providing access to various metrics and external experimental resources for structure evaluation.
  • Implementing carbohydrate-specific methods for assessing structural quality.

Main Results:

  • The Privateer database offers enhanced access to quality indicators for glycan structures.
  • It links to external resources, enabling comprehensive structure validation.
  • The tool facilitates the identification of potentially problematic carbohydrate structures.

Conclusions:

  • The Privateer database is a valuable free resource for the scientific community.
  • It addresses the need for improved quality assessment of glycan structures in the PDB.
  • Enhanced validation tools promote more accurate interpretation of glycan data.