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RNA structures (DSSR) / Re: How the length of the sequence depends on _pdbx_unobs_or_zero_occ_atoms ???
« Last post by xiangjun on September 05, 2024, 10:58:42 pm »Hi,
DSSR is based on 3D structures of DNA/RNA, deriving features of base-pairing and stacking interactions. It also takes abasic sites into consideration in later releases, requiring only P or at least 5 out of the 6 main-chain backbone atoms (P, O5', C5', C4', C3', and O3'). In PDB entry 4AL5, nucleotide C4 has only one backbone atom (O3'), and C21 has 4 backbone atoms (P, O1P, O2P, and O5') as shown below.
So in previous DSSR versions, both nucleotides are ignored.
Following your question, I've revised DSSR to v2.4.4-2024sep06 which can recognize these two nucleotides. See below:
Best regards,
Xiang-Jun
DSSR is based on 3D structures of DNA/RNA, deriving features of base-pairing and stacking interactions. It also takes abasic sites into consideration in later releases, requiring only P or at least 5 out of the 6 main-chain backbone atoms (P, O5', C5', C4', C3', and O3'). In PDB entry 4AL5, nucleotide C4 has only one backbone atom (O3'), and C21 has 4 backbone atoms (P, O1P, O2P, and O5') as shown below.
ATOM 2826 O "O3'" . C B 2 3 ? 14.682 -18.630 19.841 1.00 152.11 ? 4 C B "O3'" 1
......
ATOM 3343 P P . C B 2 20 ? 2.515 -3.243 14.608 1.00 43.27 ? 21 C B P 1
ATOM 3344 O OP1 . C B 2 20 ? 1.257 -3.732 14.022 1.00 60.70 ? 21 C B OP1 1
ATOM 3345 O OP2 . C B 2 20 ? 2.599 -1.863 15.133 1.00 37.31 ? 21 C B OP2 1
ATOM 3346 O "O5'" . C B 2 20 ? 2.975 -4.175 15.812 1.00 40.82 ? 21 C B "O5'" 1
So in previous DSSR versions, both nucleotides are ignored.
Following your question, I've revised DSSR to v2.4.4-2024sep06 which can recognize these two nucleotides. See below:
# x3dna-dssr -i=4AL5.cif
Secondary structures in dot-bracket notation (dbn) as a whole and per chain
>4AL5 nts=18 [whole]
CACUGCCGUAUAGGCAGC
..(((((.....))))).
-.AAAA..A...AAAA--
****************************************************************************
Summary of structural features of 18 nucleotides
Note: the first five columns are: (1) serial number, (2) one-letter
shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base
ring atoms fitted against those in a standard base reference
frame. The sixth (last) column contains a comma-separated list of
features whose meanings are mostly self-explanatory, except for:
turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees
break: no backbone linkage between O3'(i-1) and P(i)
1 C . B.C4 --- non-stack,ss-non-loop
2 A . B.A5 0.013 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart
3 C ( B.C6 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart
4 U ( B.U7 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate
5 G ( B.G8 0.015 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate
6 C ( B.C9 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate
7 C ( B.C10 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop,phosphate
8 G . B.G11 0.043 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,cap-acceptor,phosphate
9 U . B.U12 0.019 turn,u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop
10 A . B.A13 0.022 u-turn,anti,~C3'-endo,non-pair-contact,hairpin-loop,cap-donor,phosphate
11 U . B.U14 0.006 turn,u-turn,anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate,splayed-apart
12 A . B.A15 0.007 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop,splayed-apart
13 G ) B.G16 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop
14 G ) B.G17 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem
15 C ) B.C18 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem
16 A ) B.A19 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem
17 G ) B.G20 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end
18 C . B.C21 --- non-stack,ss-non-loop,phosphate
Best regards,
Xiang-Jun