**************************************************************************** DSSR: a software program for Defining the Secondary Structures of RNA from three-dimensional coordinates v1.2.1-2015feb01, Xiang-Jun Lu (xiangjun@x3dna.org) This program is being actively maintained and developed. As always, I greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (forum.x3dna.org). I strive to respond *promptly* to *any questions* posted there. **************************************************************************** Note: Each nucleotide is identified by model:chainId.name#, where the 'model:' portion is omitted if no model number is available (as is often the case for x-ray crystal structures in the PDB). So a common example would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are always welcome on the 3DNA Forum. Command: x3dna-dssr -i=1ymo.pdb --idstr=short -o=1ymo.out Date and time: Sat Jan 31 23:21:03 2015 File name: 1ymo.pdb no. of DNA/RNA chains: 1 [A=47] no. of nucleotides: 47 no. of atoms: 1497 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 24 base pairs nt1 nt2 bp name Saenger LW DSSR 1 G1 C29 G-C WC 19-XIX cWW cW-W 2 G2 C28 G-C WC 19-XIX cWW cW-W 3 G3 C27 G-C WC 19-XIX cWW cW-W 4 C4 G26 C-G WC 19-XIX cWW cW-W 5 U5 A25 U-A WC 20-XX cWW cW-W 6 U5 A35 U+A -- n/a cSH cm+M 7 G6 C24 G-C WC 19-XIX cWW cW-W 8 G6 A36 G+A -- 10-X tSW tm+W 9 U7 A37 U+A Hoogsteen 23-XXIII cWH cW+M 10 U8 A38 U+A Hoogsteen 23-XXIII cWH cW+M 11 U9 A39 U+A Hoogsteen 23-XXIII cWH cW+M 12 U10 A40 U+A Hoogsteen 23-XXIII cWH cW+M 13 U11 A40 U+A -- n/a cWH cW+M 14 G15 C46 G-C WC 19-XIX cWW cW-W 15 C16 G45 C-G WC 19-XIX cWW cW-W 16 U17 A44 U-A WC 20-XX cWW cW-W 17 G18 C43 G-C WC 19-XIX cWW cW-W 18 A19 U42 A-U WC 20-XX cWW cW-W 19 C20 G41 C-G WC 19-XIX cWW cW-W 20 U21 A40 U-A WC 20-XX cWW cW-W 21 U22 A39 U-A WC 20-XX cWW cW-W 22 U23 A38 U-A WC 20-XX cWW cW-W 23 C24 A37 C-A -- n/a cSW cm-W 24 G26 A33 G-A Sheared 11-XI tSH tm-M **************************************************************************** List of 6 multiplets 1 nts=3 CGA C4,G26,A33 2 nts=3 UAA U5,A25,A35 3 nts=3 GCA G6,C24,A36 4 nts=3 UUA U8,U23,A38 5 nts=3 UUA U9,U22,A39 6 nts=3 UUA U10,U21,A40 **************************************************************************** List of 1 helix Note: a helix is defined by base-stacking interactions, regardless of bp type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[2] bps=16 strand-1 5'-GGGCUGUAAAGUCAGC-3' bp-type ||||||.||||||||| strand-2 3'-CCCGACAUUUCAGUCG-5' helix-form ...AAxx...AA..A 1 G1 C29 G-C WC 19-XIX cWW cW-W 2 G2 C28 G-C WC 19-XIX cWW cW-W 3 G3 C27 G-C WC 19-XIX cWW cW-W 4 C4 G26 C-G WC 19-XIX cWW cW-W 5 U5 A25 U-A WC 20-XX cWW cW-W 6 G6 C24 G-C WC 19-XIX cWW cW-W 7 U7 A37 U+A Hoogsteen 23-XXIII cWH cW+M 8 A38 U23 A-U WC 20-XX cWW cW-W 9 A39 U22 A-U WC 20-XX cWW cW-W 10 A40 U21 A-U WC 20-XX cWW cW-W 11 G41 C20 G-C WC 19-XIX cWW cW-W 12 U42 A19 U-A WC 20-XX cWW cW-W 13 C43 G18 C-G WC 19-XIX cWW cW-W 14 A44 U17 A-U WC 20-XX cWW cW-W 15 G45 C16 G-C WC 19-XIX cWW cW-W 16 C46 G15 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems Note: a stem is defined as a helix consisting of only canonical WC/wobble pairs, with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=6 strand-1 5'-GGGCUG-3' bp-type |||||| strand-2 3'-CCCGAC-5' helix-form ...AA 1 G1 C29 G-C WC 19-XIX cWW cW-W 2 G2 C28 G-C WC 19-XIX cWW cW-W 3 G3 C27 G-C WC 19-XIX cWW cW-W 4 C4 G26 C-G WC 19-XIX cWW cW-W 5 U5 A25 U-A WC 20-XX cWW cW-W 6 G6 C24 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=9 strand-1 5'-GCUGACUUU-3' bp-type ||||||||| strand-2 3'-CGACUGAAA-5' helix-form A..AA... 1 G15 C46 G-C WC 19-XIX cWW cW-W 2 C16 G45 C-G WC 19-XIX cWW cW-W 3 U17 A44 U-A WC 20-XX cWW cW-W 4 G18 C43 G-C WC 19-XIX cWW cW-W 5 A19 U42 A-U WC 20-XX cWW cW-W 6 C20 G41 C-G WC 19-XIX cWW cW-W 7 U21 A40 U-A WC 20-XX cWW cW-W 8 U22 A39 U-A WC 20-XX cWW cW-W 9 U23 A38 U-A WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 4 stacks Note: a stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. -------------------------------------------------------------------- 1 nts=2 UU U10,U11 2 nts=2 AA A31,A32 3 nts=2 AA A37,A38 4 nts=6 UUAACA U8,U7,A36,A35,C34,A33 ----------------------------------------------------------------------- Nucleotides not involved in stacking interactions nts=9 UUCUUCCCA U9,U13,C14,U22,U23,C24,C30,C43,A47 **************************************************************************** Note: for the various types of loops listed below, numbers within the first set of brackets are the number of loop nts, and numbers in the second set of brackets are the identities of the stems (positive number) or isolated WC/wobble pairs (negative numbers) to which they are linked. **************************************************************************** List of 2 hairpin loops 1 hairpin loop: nts=19; [17]; linked by [#1] nts=19 GUUUUUCUCGCUGACUUUC G6,U7,U8,U9,U10,U11,C12,U13,C14,G15,C16,U17,G18,A19,C20,U21,U22,U23,C24 nts=17 UUUUUCUCGCUGACUUU U7,U8,U9,U10,U11,C12,U13,C14,G15,C16,U17,G18,A19,C20,U21,U22,U23 2 hairpin loop: nts=16; [14]; linked by [#2] nts=16 UCAGCCCCAAACAAAA U23,C24,A25,G26,C27,C28,C29,C30,A31,A32,A33,C34,A35,A36,A37,A38 nts=14 CAGCCCCAAACAAA C24,A25,G26,C27,C28,C29,C30,A31,A32,A33,C34,A35,A36,A37 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=1 A A47 **************************************************************************** This structure contains 1-order pseudoknot o You may want to run DSSR again with the '--nested' option which removes pseudoknots to get a fully nested secondary structure representation. **************************************************************************** List of 3 H-type pseudoknot loop segments 1 stem#1(hairpin#1) vs stem#2(hairpin#2) L1 groove=MAJOR nts=8 UUUUUCUC U7,U8,U9,U10,U11,C12,U13,C14 2 stem#1(hairpin#1) vs stem#2(hairpin#2) L2 groove=----- nts=0 3 stem#1(hairpin#1) vs stem#2(hairpin#2) L3 groove=minor nts=8 CAAACAAA C30,A31,A32,A33,C34,A35,A36,A37 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1ymo nts=47 [whole] GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAGUCAGCA [[[[[[........(((((((((]]]]]]........))))))))). >1ymo-1-A #1 nts=47 [chain] RNA GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAGUCAGCA [[[[[[........(((((((((]]]]]]........))))))))). **************************************************************************** List of 10 additional files 1 1ymo-stems.pdb -- an ensemble of stems 2 1ymo-helices.pdb -- an ensemble of helices (coaxial stacking) 3 1ymo-pairs.pdb -- an ensemble of base pairs 4 1ymo-multiplets.pdb -- an ensemble of multiplets 5 1ymo-hairpins.pdb -- an ensemble of hairpin loops 6 1ymo-2ndstrs.bpseq -- secondary structure in bpseq format 7 1ymo-2ndstrs.ct -- secondary structure in connect table format 8 1ymo-2ndstrs.dbn -- secondary structure in dot-bracket notation 9 1ymo-torsions.txt -- backbone torsion angles and suite names 10 1ymo-stacks.pdb -- an ensemble of stacks