Monitoring carbohydrate 3D structure quality with the Privateer database

Introduction

Carbohydrate modelling is an important but often cumbersome stage in the macromolecular X-ray structure solution workflow. The accurate modelling of glycoproteins and protein–carbohydrate complexes is pivotal in understanding the complex biochemical interactions that affect the physiological function of cells [1]. Any mechanistic analysis done with finely grained approaches such as QM/MM [2] relies heavily on the correctness of the starting coordinates. Despite this, carbohydrate models often contain modelling inconsistencies that cannot easily be attributed to known biochemical principles [3]. These inconsistencies cannot solely be attributed to model-building inexperience, as carbohydrate model building is an inherently difficult task, which in the past has been plagued with software related problems from incorrect libraries to incomplete support [4]. Carbohydrates are mobile, highly branched additions to the comparatively rigid protein framework; in macromolecular crystallography, this causes heterogeneity throughout the crystal lattice and, therefore, poorly resolved density regions, whereas in electron cryo-microscopy different conformations and compositions are averaged out during image classification and volume reconstruction [5].

Owing to these difficulties, it is not uncommon to find problematic carbohydrate structures in the Protein Data Bank (PDB), from the initial works of Lütteke, Frank and von der Lieth [6,7], who identified numerous issues affecting nomenclature and linkages (estimated to affect 30% of the structures at the time), to the reports of surprising – or indeed glyco-chemically impossible – linkages in a glycoprotein as pointed out by Crispin and collaborators [8], and more recently the realisation that high-energy ring conformations, a rare event in six-membered pyranosides, were present in ca. 15% of the N-glycan components of glycoproteins in the PDB [3]. Many of these findings originated the development of new resources, including services and databases [9-13], and standalone software [14-18]. Among these, the Privateer software package has been a key tool for glycoprotein and protein–carbohydrate complex validation: Privateer analyses the conformational plausibility of each sugar model [3], checks that structures match the nomenclature used for deposition in the PDB [14], compares glycan compositions to known structures as reported by glycomics (e.g., GlyConnect [19]) and glyco-informatics (e.g., GlyTouCan [20]) databases and repositories [15], and checks how close the overall conformation of N-glycans comes to that of validated deposited structures [16].

The PDB-REDO [21] database is a separate resource, albeit linked to the PDB in that the entries that compound PDB-REDO are those original PDB crystallographic entries that included experimental data (i.e., reflection intensities or amplitudes); each entry includes a re-refined, sometimes even re-built to some extent, copy of the original model. These newer versions are produced with state-of-the-art methods, many of which were probably not available at the time of deposition; hence, the quality of the models is expected to improve. Because the methodology included in PDB-REDO had been affected by the lack of automatic support that plagued general purpose crystallographic model building and refinement software [4], carbohydrate-specific methods have been gradually introduced over the years [22,23].

Whilst Privateer has been a staple tool in carbohydrate validation, the results of Privateer have not been collated in such a way that allows for easy judgement of carbohydrate model quality in the PDB [24]. Providing users with metrics that allow them to make chemically sound conclusions about the model is an important facility, especially for novice users. To allow this to happen readily on PDB distribution sites, we present the Privateer database, a freely available, up-to-date collection of validation information for both the PDB and PDB-REDO [21] archives.

Results and Discussion

Format of the validation report

The JSON file deposited for each PDB entry follows a consistent format, as shown in Figure 1. At the top level, the file contains metadata about the validation report. This metadata provides the date that the validation report was generated as well as the availability of experimental data. It is helpful to have this information easily accessible as Privateer cannot calculate the real space correlation coefficient without experimental data; therefore, programmatic access to further validation metrics could be streamlined, knowing the information is not present.

Also at the top level of the validation report is the beginning of the carbohydrate information, listed as ‘glycans’ in the JSON format. Within this ‘glycan’ scope, information is segmented into glycan types, that is, ‘n-glycan’, ‘o-glycan’, ‘s-glycan’, ‘c-glycan’, and 'ligand'. Each of these glycan types contains an array of individual glycans of that type, and the format of the data inside each of these glycan types is identical.

The data contained in each glycan entry is shown in Table 1. Each entry contains information about the protein chain attachment, the number of sugars in the glycan, the WURCS2.0 code [25], the standard nomenclature for glycan SVG, and an array of sugar entries. The validation data calculated by Privateer for each sugar entry is shown in Table 2, and that for each linkage is shown in Table 3.

Visualising a validation report

While the database is available on GitHub for programmatic access, viewing a validation report entry in plaintext can be difficult, time-consuming and would certainly be a poor experience for the end user. To improve the utility of this database, we have provided a visualisation of the information contained within the validation report for both PDB and PDB-REDO databases, which is available alongside the Privateer Web App [26], https://privateer.york.ac.uk/database.

The first section of this visual report displays a global outlook on the validity of the model through two graphs. The first graph shows the conformational landscape for the pyranose sugars. For a sugar model to be deemed valid, the ring must be in the ⁴C₁ chair conformation. This can be measured through the Cremer–Pople parameters θ and ψ [27]. Theta angles of 0° < θ < 360° indicate that the sugar may be in a higher-energy confirmation; therefore, caution should be placed on any conclusions drawn from the molecular model of the sugar. Also in the first section of the visual validation report is a plot of the B-factor (temperature factor) versus the real space correlation coefficient (RSCC) (Figure 2). A well-refined, well-built model would be expected to have a B-factor that increases somewhat linearly as the RSCC decreases. Over-refined models may deviate from this trend and would be trivial to identify.

The validation report also displays a table (Figure 3) representing two-dimensional descriptions of each glycan in the model. Each row in the table represents a unique glycan and includes the chain identifier, standard Symbol Nomenclature for Glycans (SNFG [29]) visualisation, and copyable WURCS [25] identifier. The SNFG displayed for each glycan paints a picture of how well built the glycan model is, as the metrics and validity conclusions calculated by Privateer are embedded within each shape and linkage of the diagram. For example, a shape with an orange highlight indicates something is abnormal about the ring’s conformation, puckering, or monosaccharide nomenclature [30]. Similarly, a linkage with an orange highlight indicates that the torsion angles between the linkages are unexpected and require further inspection [16].

In addition to the SNFG, also displayed for each table entry is a copyable WURCS link, which encodes the complete glycan format in a linear code. The decision to present this information as a copyable link, as opposed to as plaintext is due to the inherent difficulty and unlikeliness for a human to read and understand the WURCS code. It is much more likely that the WURCS code would be copied and searched for in a glycomics database, hence we provide that functionality in a streamlined way.

The final section of the validation report includes all of the validation metrics calculated by Privateer and, most importantly, the diagnostic provided by Privateer (Figure 4). A ‘yes’ diagnostic indicates the conformation is correct for the glycosylation type (e.g., ⁴C₁ for GlcNAc in an N-glycan, ¹C₄ for mannose in a C-glycan), has the correct anomer, and has an acceptable fit to density. This diagnostic indicates that the sugar is valid, whereas a diagnostic of ‘check’ indicates that Privateer has detected a potential inconsistency affecting ring conformation, which requires manual inspection. Finally, a ‘no’ diagnostic indicates that the sugar needs a more detailed manual inspection to correct any conformational issues, anomeric issues, or fitting issues.

Searching for entries in the Privateer database

Another interesting application of the collection of data available in the Privateer database is to visualise aggregated carbohydrate data from the PDB. Using the search interface on the Privateer database homepage, carbohydrate-containing PDB entries can easily be found and filtered. Privateer database entries for specific glycosylation types, namely, N-glycosylation, O-glycosylation, S-glycosylation, or C-glycosylation can be filtered quickly and easily. Additional filtering by linkage type is also possible, allowing niche glycosylation targets to be obtained. For example, filtering for C-glycans with a ‘BMA-1,1-TRP’ (the correct pair would be ‘MAN-1,1-TRP’, as the linkage in the modification is an alpha linkage) returns nine instances of incorrect sugar conformations in C-mannosylation found within the Privateer database in a table containing the frequency of the target linkage as well as a link to the Privateer database report page for target entry (Figure 5). This table view is also keyword or range-filterable at every data column, which allows for trivial searches of potentially interesting models.

Trends in the Privateer database

Using the Privateer database, global statistics throughout the PDB and PDB-REDO can be calculated with ease. Observing deposition trends in the PDB is often interesting as it can provide insight into the kinds of structures that are experimentally obtainable over time. With the Privateer database, trends in glycosylation deposition in the PDB over time can be measured, as shown in Figure 6. Importantly, as the Privateer database is completely recompiled every week, these trends remain consistent with the PDB. To allow for easy and up-to-date observation for anyone, compiled statistics are freely available alongside the Privateer Web App, https://privateer.york.ac.uk/statistics.

While simply looking at glycosylation over time using the Privateer database is possible, the validation reports calculated by Privateer contain a whole host of other interesting pieces of information. In an analogous way to looking at glycosylation over time, the type and validity of carbohydrates in the PDB can also be observed over time. The statistics page available alongside the Privateer Web App contains up-to-date plots of validation and conformational errors over time and resolution.

Conclusion

In conclusion, the new Privateer database encompasses the carbohydrate validation capabilities of Privateer in an easily accessible pre-prepared form. The database contains all validation metrics calculated by Privateer as well as highlighted SNFG diagrams in SVG format for easy third-party web use. Statistics are automatically computed weekly and are available alongside the database both on GitHub and the interactive web page.

Materials and Methods

The Privateer software package [14] was used to compute metrics and statistics for each entry in the PDB [24] or in PDB-REDO [21]. For each structure in the PDB, the carbohydrate-containing chains are first identified before being validated using the suite of validation tools available within Privateer. Using the Python bindings available within the latest versions of Privateer, a validation report can be generated for each carbohydrate in the molecular model. This report is put out in JSON format for easy consumption by web-based database frontends. The initial report generation was completed in parallel over 64 CPU cores in around 5 h. After the initial surveys through PDB and PDB-REDO, this process only needs to be completed when new molecular models are deposited into the PDB, which occurs weekly. Although compiling validation reports for only new structures would be more efficient, this would fail to encompass changes in structures in historical entries, therefore the Privateer database is recompiled weekly.

The database, which receives any updates to the reports after recompilation is hosted on GitHub. The database is separated into PDB and PDB-REDO sections, which are in turn structured in the same format as the PDB archive, separated into folders by the middle two characters of the PDB four-letter code. For convenience, the presentation of the database is hosted alongside the Privateer Web App [26]; the database part can be accessed at https://privateer.york.ac.uk/database or by navigating to the database icon on the top right of the screen. The website is dynamic and compatible with desktop and laptop computers, plus tablets and smartphones.