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. 2020 Sep 1;76(Pt 9):805-813.
doi: 10.1107/S2059798320009389. Epub 2020 Aug 17.

Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org

Jiří Černý  1 , Paulína Božíková  1 , Michal Malý  1 , Michal Tykač  1 , Lada Biedermannová  2 , Bohdan Schneider  2
Affiliations

Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org

Jiří Černý et al. Acta Crystallogr D Struct Biol. .

Abstract

A detailed description of the dnatco.datmos.org web server implementing the universal structural alphabet of nucleic acids is presented. It is capable of processing any mmCIF- or PDB-formatted files containing DNA or RNA molecules; these can either be uploaded by the user or supplied as the wwPDB or PDB-REDO structural database access code. The web server performs an assignment of the nucleic acid conformations and presents the results for the intuitive annotation, validation, modeling and refinement of nucleic acids.

Keywords: annotation; nucleic acids; refinement; structural alphabets; validation.

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Figures

Figure 1
Figure 1
The dinucleotide step is defined by (i) seven backbone torsions, (ii) two torsions around the glycosidic bonds, (iii) one pseudo-torsion angle and (iv) two distances. The atoms involved are (i) δ1, C5′(1)—C4′(1)—C3′(1)—O3′(1); ∊1, C4′(1)—C3′(1)—O3′(1)—P(2); ζ1, C3′(1)—O3′(1)—P(2)—O5′(2); α2, O3′(1)—P(2)—O5′(2)—C5′(2); β2, P(2)—O5′(2)—C5′(2)—C4′(2); γ2, O5′(2)—C5′(2)—C4′(2)—C3′(2); δ2, C5′(2)—C4′(2)—C3′(2)—O3′(2) and (ii) χ1, O4′(1)—C1′(1)—N1/9(1)—C2/4(1); χ2, O4′(2)—C1′(2)—N1/9(2)—C2/4(2). (iii) The pseudo-torsion μ is defined as torsion between the atoms defining the glycosidic bonds of the first and second nucleotides: N1/N9(1)—C1′(1)—C1′(2)—N1/N9(2). (iv) The two distances are N1/9(1)—N1/9(2) and C1′(1)—C1′(2).
Figure 2
Figure 2
Snapshot of the Front page showing the tabs (labeled 1–8) at the top of the page as described in more detail in Section 3.1. The middle part shows the definition of a dinucleotide step with 12 parameters (white text for torsions and blue for distances) and the 18 atoms (green spheres) necessary for their calculation. The bottom part of the page allows the upload of user-provided coordinates (A) or the analysis of database-deposited structures (B).
Figure 3
Figure 3
Snapshot of the Results page showing a typical representation of the conformations assigned to a nucleic acid structure. The sarcin/ricin loop structure with PDB code 1q93 (Correll et al., 2003 ▸) is used as an example. The figure demonstrates the intuitive annotation and simple recognition of structural features and motifs in the structure. The regions labeled 1–6 are described in more detail in Section 3.2.
Figure 4
Figure 4
Enlargement of the selected 1q93_A_G14_A15 step, showing the details of the overlapping reference steps AA00 (blue sticks) for G13_G14, OP03 (green sticks) for G14_A15 and AA00 (cyan sticks) for A15_G16. With the ‘contacts’ checkbox active, the residues and atoms around the selected step are shown in gray. The density-map sigma as well as the slab-control values are set for clarity.
Figure 5
Figure 5
A collage of detailed results for the 1q93_A_G14_A15 step. The regions labeled 1–8 are described in more detail in Section 3.3.
Figure 6
Figure 6
Analysis of similarity (1) and connectivity (2) plots for the 1q93_A_C18_G19 step. The similarity plot shows a relatively common case in which a range of NtC conformers, AA08, AA00, AA03, AA09, AA04, AB05 and so on, share a similar overall 3D shape as given by the Cartesian r.m.s.d. value. These cases in general show the strength of the backbone torsion-based assignment process in distinguishing the most probable conformational class of the step from the set of populated clusters.
Figure 7
Figure 7
A collage of detailed results for the 1q93_A_C18_G19 step. The regions labeled 1–3 are described in more detail in Section 3.4.
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