Abstract
Glycosylation is one of the most common forms of protein post-translational modification, but is also the most complex. Dealing with glycoproteins in structure model building, refinement, validation and PDB deposition is more error-prone than dealing with nonglycosylated proteins owing to limitations of the experimental data and available software tools. Also, experimentalists are typically less experienced in dealing with carbohydrate residues than with amino-acid residues. The results of the reannotation and re-refinement by PDB-REDO of 8114 glycoprotein structure models from the Protein Data Bank are analyzed. The positive aspects of 3620 reannotations and subsequent refinement, as well as the remaining challenges to obtaining consistently high-quality carbohydrate models, are discussed.
Highlights
Structural biology provides us with insight into the molecular mechanisms of life (Branden & Tooze, 1998)
Dealing with glycoproteins in structure model building, refinement, validation and Protein Data Bank (PDB) deposition is more error-prone than dealing with nonglycosylated proteins owing to limitations of the experimental data and available software tools
The glycan parts of these structures often feature many flaws ranging from minor irregularities to gross errors (Lutteke et al, 2004; Crispin et al, 2007; Agirre, Davies et al, 2015). This problem has multiple causal factors: the median data resolution of glycoproteins (2.4 A ) is somewhat lower than that of PDB entries in general (2.0 A ); most software tools for structural biology are protein-centric and do not deal with carbohydrates as well as they deal with proteins; most crystallographers are less well trained in dealing with carbohydrates; glycosylation sites on a protein may not be part of the research question for which a structure is solved; validation of carbohydrates is not part of the standard structure-elucidation process; and the deposition and annotation process of the wwPDB (Young et al, 2017) is not focused on carbohydrates
Summary
Structural biology provides us with insight into the molecular mechanisms of life (Branden & Tooze, 1998). The glycan parts of these structures often feature many flaws ranging from minor irregularities to gross errors (Lutteke et al, 2004; Crispin et al, 2007; Agirre, Davies et al, 2015) This problem has multiple causal factors: the median data resolution of glycoproteins (2.4 A ) is somewhat lower than that of PDB entries in general (2.0 A ); most software tools for structural biology are protein-centric and do not deal with carbohydrates as well as they deal with proteins; most crystallographers are less well trained in dealing with carbohydrates; glycosylation sites on a protein may not be part of the research question for which a structure is solved (that is, little effort is spent on these); validation of carbohydrates is not part of the standard structure-elucidation process; and the deposition and annotation process of the wwPDB (Young et al, 2017) is not focused on carbohydrates. We use this opportunity to see where PDB-REDO stands in terms of the various aspects of carbohydrate structure model quality and what more can be improved in future incarnations of the PDB-REDO project
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