In DSSR, the --frame option allows users to reorient a nucleic acid structure using the standard base reference frame (see Olson et al., 2001). This option can be applied not only to an individual base frame but also a base-pair frame, or the middle frame between two bases or base pairs. These variations facilitate the alignment of nucleic acid structures for a wide range of comparative analyses. In this blog post, I will demonstrate how to use the --frame option with concrete examples, enabling readers to apply this unique DSSR feature to their own projects.

The standard base reference frame

The standard base reference frame is derived from an idealized Watson-Crick base pairing geometry (top-left, figure below). The x-axis points in the direction of the major groove along what would be its pseudo-dyad axis—that is, the perpendicular bisector of the C1'...C1' vector spanning the base pair. The y-axis runs along the long axis of the idealized base-pair in the direction of the sequence strand, parallel to the C1'...C1' vector, and is displaced so as to pass through the intersection between the (pseudo-dyad) x-axis and the vector connecting the pyrimidine Y(C6) and purine R(C8) atoms. The z-axis is defined by the right-handed rule. For right-handed A- and B-DNA, the z-axis accordingly points along the 5' to 3' direction of the sequence strand.

Typical usages of the --frame option

Using the classic B-DNA dodecamer PDB entry 355d as an example, DSSR can be run with the --frame option as follows:

#             1...5..8....
# chain A: 5'-CGCGAATTCGCG -3'
# chain B: 3'-GCGCTTAAGCGC -5'

# reorient 355d in the reference frame of C1 on chain A
x3dna-dssr -i=355d.pdb --frame=A.1 -o=355d-b1.pdb

# reorient 355d in the frame of the Watson-Crick pair C1-G24
x3dna-dssr -i=355d.pdb --frame=A.1:wc -o=355d-bp1.pdb

#  ... with the minor-groove of pair C1-G24 facing the viewer
x3dna-dssr -i=355d.pdb --frame=A.1:wc-minor -o=355d-bp1-minor.pdb

# with the minor-groove of the middle AATT tract facing the viewer
x3dna-dssr -i=355d.pdb --frame='A.5:wc-minor A.8:wc' -o=355d-AATT-minor.pdb

# Rendered in cartoon-blocks with base-pair blocks, and black minor-groove
# Load 355d-AATT-minor.pml into PyMOL (bottom-left, figure above)
x3dna-dssr -i=355d-AATT-minor.pdb --cartoon-block --block-file=wc-minor -o=355d-AATT-minor.pml

The abbreviated notation A.1 refers to nucleotide numbered 1 (as indicated in the coordinates file) on chain A. Here, it denotes C1, as shown at the top of the listing. Similarly, A.5 and A.8 correspond to nucleotides A5 and T8 on chain A, respectively. In most cases, such as with 355d, the combination of chain identifier and residue number is sufficient to uniquely identify a nucleotide. More generally, other information such as model number or insertion code may be needed to specify a particular nucleotide.

In the above listing, wc after the colon (for example, A.1:wc) specifies the Watson-Crick base pair that the corresponding nucleotide participates in. Meanwhile, minor transforms the structure so that the minor-groove of the base (or base pair, or step) faces the viewer. The keywords wc and minor are settings that influence the construction or view of the frame. Case or order does not matter for these keywords as long as there is a match—for example, minor+wc works the same as wc-minor.

Two other examples combining the --frame option with cartoon-block representations

The intuitive geometric meaning of the standard base reference frame combined with the DSSR-enabled cartoon-block representation allows for an enhanced understanding of intricate structural features. In the top-right panel of the figure above, we see the classic yeast phenylalanine tRNA (PDB entry 1ehz) viewed into the minor-groove of the pseudo-knotted G19-C56 pair at the elbow of the L-shaped tertiary structure. The stacking interactions of the purines at the top-right of the panel are clearly visible in this view. In the bottom-right panel, an anti-parallel G-quadruplex from PDB entry 8ht7 is shown. The G-tetrads are automatically identified and rendered as square blocks, all with DSSR. This representation makes the chair conformation of the three-layered anti-parallel G-quadruplex crystal clear. The DSSR commands used are listed below:

# yeast tRNA (1ehz)
x3dna-dssr -i=1ehz.pdb --frame=A.19:wc-minor -o=1ehz-elbow.pdb
x3dna-dssr -i=1ehz-elbow.pdb --cartoon-block --block-file=wc-minor -o=1ehz-elbow.pml

# anti-parallel chair-shaped G-quadruplex (8ht7)
x3dna-dssr -i=8ht7.pdb --select=nts -o=8ht7-nts.pdb  # extract nucleotides, ignore amino acids
# reorient 8ht7 in the frame of the G-tetrad involving G1, in edge view
x3dna-dssr -i=8ht7-nts.pdb --frame=A.1:G4-minor -o=8ht7-Gtetrad.pdb
x3dna-dssr -i=8ht7-Gtetrad.pdb --block-cartoon --block-file=G4-minor -o=8ht7-Gtetrad.pml

References

Olson,W.K. et al. (2001) A standard reference frame for the description of nucleic acid base-pair geometry. Journal of Molecular Biology, 313, 229–237.