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1
Hi Xiang-Jun,

We just came across a strange sequence and dot-bracket notation for the dssr output.
open http://dssr.x3dna.org/ , type in 4v91, go the Secondary structures in dot-bracket notation section. You will see something as following:

>4v91 nts=3482 [whole]
U&U&GACCUCA&AA&UCAGGUAGGAGUACCCG&CUGA&AC&UUAAGCAU&AUCAAUAAGCG&G

A lot of "&"s  are inserted in sequence and dot-bracket notation. It looks like a bug for the output.

Best,
Shuxiang

2
Figure 6. Molecular images of multiplets with two or more modes of G·A pairing in the complex of tetracycline with the U1052G-mutated 70S Escherichia coli ribosome.(69) Loops incorporating m–M sheared pairs are linked by different associations of G and A (highlighted within boxes) to other secondary structural units. A local representation of the linked bases is shown below each global depiction of associated secondary structures. Examples include (a) tetraplex with m+m pairing between a hairpin loop and a double-helical stem, (b) tetraplex with m+m pairing between an internal loop and a double-helical stem, (c) pentaplex with m+W pairing between a hairpin loop and a double-helical stem that is linked in turn to a junction, (d) tetraplex with m–m link pairing between an internal loop and a 5-way junction, (e) triplex with m–W pairing between a hairpin loop and a 3-way junction, and (f) pentaplex with .–M and m–W pairing within a 7-way junction. G·A pairs and secondary structural motifs are color-coded as in Figure 2. See Table S3 for respective Protein Data Bank identifiers, chain names, and residue numbers of depicted G·A-linked multiplets. Color-coding of bases and hydrogen bonds matches that in the corresponding secondary structural diagrams in Figure S8.

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Figure 5. Molecular images illustrating hydrogen bonds (dashed lines) shared between different forms of G·A pairing: (a) N3···N6 interaction common to m–WII and m–MI base-paired arrangements found in a variant of the SAM-I riboswitch(64) and the complex of Escherichia coli ribosomal protein L25 with a 5S rRNA fragment, respectively;(65) (b) respective N2···N1 associations in m–WI and W–W pairs in the Leishmania donovani large ribosomal subunit(66) and the Saccharomyces cerevisiae 80S ribosome;(67) (c) N2···N7, N1···OP2, and N2···OP2 hydrogen bonds stabilizing W–M and m–MII pairs in the central domain of the Thermus thermophilus 30S ribosomal subunit(68) and in the complex of the Thermus thermophilus 70S ribosome with hibernation factor pY, respectively;(36) (d) respective paired association of 2′-hydroxyl groups, one from G and the other from A, adopted in m–m and m–WI pairs within the complex of tetracycline with the U1052G-mutated 70S Escherichia coli ribosome.(69)

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Figure 4. Succession of configurations illustrating the rigid-body motions that transform the associations of G and A between different pairing modes. Images are of adenine oriented with respect to a common coordinate frame on guanine. Structures are generated with 3DNA(24) using the average rigid-body parameters reported in Table 1. Base pairs are color-coded by interaction mode (Figures 1–3), with the minor (II) substates of m±W and m–M pairs noted by lighter hues. Pathways connect (a) antiparallel m–m, m–WI, m–WII, W–W, m–MI, and m–MII states and (b) parallel m+m, m+WII, m+WI, and m+M states. Note the counterclockwise rotation of ribose C1′ atoms (darkened spheres) along the top-to-bottom transformation of antiparallel pairs and the clockwise rotation along the corresponding progression of parallel pairs. Hydrogen bonds between base atoms are depicted by thin dashed lines.

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Figure 3. Scatter plots of the rigid-body components—shear, stretch, and opening—that distinguish the modes of G·A association in RNA-containing structures. Smooth curves on the edges of the scatter plots are the normalized densities of individual parameters. Points with the magnitude of opening in excess of 180° include requisite changes in the signs of shear, stretch, buckle, and propeller. Color-coding of dominant pairs matches that in Figures 1 and 2. Secondary states with 16 or more structural examples are noted by related hues. Images depict the spread of values in the shear–opening (left) and shear–stretch (right) planes for antiparallel G–A (top) and parallel G+A (bottom) arrangements.

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Figure 2. Molecular images of RNA secondary structural motifs incorporating each of the dominant modes of G·A base pairing. Motifs correspond to one of the common settings of the designated pairs: (a) sheared m–M pair closing the GNRA tetraloop at the end of the P4 helix of the glmS ribozyme bound to glucosamine 6-phosphate;(35) (b) imino W–W pair at the end of an asymmetric internal loop in the Thermus thermophilus 70S ribosome in complex with the hibernation factor pY;(36) (c) m+m pair linking the G in a double-helical stem and the A in an internal loop of the complex of Thermus thermophilus ribosomal protein L1 with a fragment of the L1 RNA from Methanoccocus vannielii;(37) (d) m–m pair joining a stem and single-stranded fragment within a three-way junction of the Thermoanaerobacter tengcongenesis ydaO riboswitch bound to cyclic di-AMP;(38) (e) m+W pair connecting the D and T hairpin loops of yeast initiator tRNA;(39) (f) m–W pair linking two hairpin loops of the 5S rRNA within the structure of the hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus.(40) The G·A pairs are color-coded as in Figure 1 and shown at the nucleotide level within each structural element and in a separate local depiction to the right of each example. Loops are depicted in gold and canonical base pairs at the ends of loops or within double-helical stems in white. Ribbons connect phosphorus atoms in successive nucleotides. See Table S3 for Protein Data Bank identifiers, chain names, and residue numbers of the depicted pairs and Figure S2 for simple secondary structural diagrams of the associated motifs.

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Figure 1. Comparison of the hydrogen-bonding interactions, chemical structures, and relative spatial arrangements of nucleotides in the six dominant modes of G·A pairing and in a canonical Watson–Crick G–C pair. Hydrogen bonds are shown by thin dashed lines, with arrows directed toward base/backbone atoms capable of accepting protons. Structures were generated with 3DNA(24) and rendered in PyMOL (www.pymol.org) using the average rigid-body parameters in Table 1 and a canonical A-RNA backbone.(34) Structures are depicted in the standard reference frame of G.(30) Color-coding denotes the mode of base association: sheared m–M (dark blue); imino W–W (gray); m+m (pink); m–m (red); m+W (light blue); m–W (magenta); canonical (white), where the combinations of signs and letters denote the orientation (parallel + /antiparallel –) and the approximate sites (minor, m; major, M; Watson–Crick, W edges) of base association.(27) Interestingly, less than 10% of the + states reflect an anti-to-syn sugar–base rearrangement, and these examples all involve adenine.

8
RNA structures (DSSR) / no nucleotide in some structures
« on: February 11, 2019, 10:24:32 am »
Hi Xiang-Jun,

I'm using DSSR to analyze some structures and it showed there is no nucleotide was found. When I visualized these structures using pymol. I indeed saw nucleotides are there. For example (6CEV):

x3dna-dssr -i=6cev.pdb

Thanks. :)

Best,
Shuxiang

9
w3DNA -- web interface to 3DNA / Web 3DNA 2.0 is up and running
« on: December 18, 2018, 09:15:17 pm »
Web 3DNA 2.0 (http://web.x3dna.org/) is a significantly enhanced interface for the analysis, visualization, and modeling of 3D nucleic-acid structures. The new server employs modern web technologies and takes advantages of the latest 3DNA version 2.4.0. As a result, the original w3DNA website (http://w3dna.rutgers.edu/) is obsolete and users are strongly encouraged to use web 3DNA 2.0 (http://web.x3dna.org/).

Web 3DNA 2.0 has six major modules: Analysis, Visualization, Rebuilding, Composite, Fiber and Mutation. Each module has its default setting and users can just click the buttons to have a feeling of what the new server has to offer.

Any questions and bug reports are welcome!

Shuxiang & Xiang-Jun

10
Hi Xiang-Jun,

I encounter a question when plotting separate frames for each base in a base pair. See the attached picture, each base has its own reference frame.


From the ref_frames.dat file, I get the information like following.  If I understand correctly, it looks like the reference frames here are the averaged frames for a base pair.
...     6 A-T   # A:...6_:[.DA]A - B:..19_:[.DT]T
   14.8825    20.6882    10.2718  # origin
    0.9873    -0.1230    -0.1006  # x-axis
   -0.0859    -0.9457     0.3135  # y-axis
   -0.1337    -0.3009    -0.9442  # z-axis

I want to obtain the reference frame for each base in a paired bases. Thank you.

Best,
Shuxiang

11
RNA structures (DSSR) / strange residue number after dssr --view option
« on: August 06, 2018, 01:10:13 pm »
Hi Xiang-Jun,

I'm using the following command to convert a DNA\protein structure into its best view conformation. (3mgp.cif is downloaded from PDB database).

x3dna-dssr -i=3mgp.cif -o=3mgp_view.cif --view

The weird thing is the residue number index of the DNA part from original file (3mgp.cif)  is from 1 to 147. However, the corresponding residue number index from best view file (3mgp_view.cif) is from -73 to 73. I'm wondering is there an opinion to keep the residue renumber same between the original file and dssr output file? Thank you. 

For example, the beginning DNA part of 3mgp.cif is:
ATOM   6161  O  "O5'" . DA  I  5 1   ? 2.638   0.163   93.308 1.00 166.52 ? -73  DA  I "O5'" 1
ATOM   6162  C  "C5'" . DA  I  5 1   ? 3.279   0.178   94.579 1.00 166.78 ? -73  DA  I "C5'" 1
ATOM   6163  C  "C4'" . DA  I  5 1   ? 3.645   -1.223  95.042 1.00 167.01 ? -73  DA  I "C4'" 1
ATOM   6164  O  "O4'" . DA  I  5 1   ? 2.489   -2.096  95.012 1.00 167.37 ? -73  DA  I "O4'" 1
ATOM   6165  C  "C3'" . DA  I  5 1   ? 4.650   -1.969  94.180 1.00 166.94 ? -73  DA  I "C3'" 1
ATOM   6166  O  "O3'" . DA  I  5 1   ? 5.972   -1.523  94.462 1.00 166.58 ? -73  DA  I "O3'" 1
ATOM   6167  C  "C2'" . DA  I  5 1   ? 4.428   -3.410  94.635 1.00 167.20 ? -73  DA  I "C2'" 1
ATOM   6168  C  "C1'" . DA  I  5 1   ? 2.941   -3.442  94.998 1.00 167.53 ? -73  DA  I "C1'" 1
ATOM   6169  N  N9    . DA  I  5 1   ? 2.097   -4.257  94.106 1.00 167.70 ? -73  DA  I N9    1
ATOM   6170  C  C8    . DA  I  5 1   ? 0.995   -3.832  93.410 1.00 167.66 ? -73  DA  I C8    1
ATOM   6171  N  N7    . DA  I  5 1   ? 0.415   -4.762  92.687 1.00 167.66 ? -73  DA  I N7    1
ATOM   6172  C  C5    . DA  I  5 1   ? 1.185   -5.889  92.920 1.00 167.82 ? -73  DA  I C5    1
ATOM   6173  C  C6    . DA  I  5 1   ? 1.094   -7.219  92.443 1.00 167.68 ? -73  DA  I C6    1
ATOM   6174  N  N6    . DA  I  5 1   ? 0.141   -7.629  91.598 1.00 167.61 ? -73  DA  I N6    1
ATOM   6175  N  N1    . DA  I  5 1   ? 2.020   -8.112  92.866 1.00 167.60 ? -73  DA  I N1    1
ATOM   6176  C  C2    . DA  I  5 1   ? 2.972   -7.698  93.715 1.00 167.61 ? -73  DA  I C2    1
ATOM   6177  N  N3    . DA  I  5 1   ? 3.161   -6.478  94.229 1.00 167.74 ? -73  DA  I N3    1
ATOM   6178  C  C4    . DA  I  5 1   ? 2.227   -5.603  93.793 1.00 167.85 ? -73  DA  I C4    1
ATOM   6179  P  P     . DT  I  5 2   ? 6.808   -0.641  93.411 1.00 166.33 ? -72  DT  I P     1
ATOM   6180  O  OP1   . DT  I  5 2   ? 6.500   0.779   93.692 1.00 166.34 ? -72  DT  I OP1   1
ATOM   6181  O  OP2   . DT  I  5 2   ? 6.588   -1.186  92.052 1.00 166.28 ? -72  DT  I OP2   1
ATOM   6182  O  "O5'" . DT  I  5 2   ? 8.341   -0.918  93.788 1.00 165.73 ? -72  DT  I "O5'" 1
ATOM   6183  C  "C5'" . DT  I  5 2   ? 8.715   -1.557  95.009 1.00 164.98 ? -72  DT  I "C5'" 1
ATOM   6184  C  "C4'" . DT  I  5 2   ? 9.072   -3.018  94.786 1.00 164.44 ? -72  DT  I "C4'" 1
ATOM   6185  O  "O4'" . DT  I  5 2   ? 7.900   -3.772  94.389 1.00 164.50 ? -72  DT  I "O4'" 1
ATOM   6186  C  "C3'" . DT  I  5 2   ? 10.122  -3.278  93.711 1.00 164.05 ? -72  DT  I "C3'" 1
ATOM   6187  O  "O3'" . DT  I  5 2   ? 11.270  -3.824  94.345 1.00 163.49 ? -72  DT  I "O3'" 1
ATOM   6188  C  "C2'" . DT  I  5 2   ? 9.469   -4.258  92.730 1.00 164.06 ? -72  DT  I "C2'" 1
ATOM   6189  C  "C1'" . DT  I  5 2   ? 8.302   -4.824  93.535 1.00 164.11 ? -72  DT  I "C1'" 1

The beginning DNA part of 3mgp_view.cif is:
ATOM   6161  O5'  DA I -73     -44.102 -28.116  24.446  1.00166.52           O
ATOM   6162  C5'  DA I -73     -45.300 -28.880  24.535  1.00166.78           C
ATOM   6163  C4'  DA I -73     -45.873 -29.191  23.161  1.00167.01           C
ATOM   6164  O4'  DA I -73     -46.042 -27.979  22.385  1.00167.37           O
ATOM   6165  C3'  DA I -73     -45.006 -30.049  22.255  1.00166.94           C
ATOM   6166  O3'  DA I -73     -45.116 -31.421  22.619  1.00166.58           O
ATOM   6167  C2'  DA I -73     -45.629 -29.773  20.889  1.00167.20           C
ATOM   6168  C1'  DA I -73     -46.128 -28.331  21.012  1.00167.53           C
ATOM   6169   N9  DA I -73     -45.409 -27.347  20.184  1.00167.70           N
ATOM   6170   C8  DA I -73     -44.776 -26.213  20.626  1.00167.66           C
ATOM   6171   N7  DA I -73     -44.212 -25.500  19.679  1.00167.66           N
ATOM   6172   C5  DA I -73     -44.491 -26.208  18.522  1.00167.82           C
ATOM   6173   C6  DA I -73     -44.167 -25.976  17.163  1.00167.68           C
ATOM   6174   N6  DA I -73     -43.462 -24.917  16.750  1.00167.61           N
ATOM   6175   N1  DA I -73     -44.595 -26.874  16.245  1.00167.60           N
ATOM   6176   C2  DA I -73     -45.305 -27.933  16.662  1.00167.61           C
ATOM   6177   N3  DA I -73     -45.667 -28.258  17.908  1.00167.74           N
ATOM   6178   C4  DA I -73     -45.229 -27.349  18.808  1.00167.85           C
ATOM   6179    P  DT I -72     -43.906 -32.208  23.323  1.00166.33           P
ATOM   6180  OP1  DT I -72     -44.062 -32.031  24.784  1.00166.34           O
ATOM   6181  OP2  DT I -72     -42.638 -31.816  22.667  1.00166.28           O
ATOM   6182  O5'  DT I -72     -44.167 -33.748  22.962  1.00165.73           O
ATOM   6183  C5'  DT I -72     -45.409 -34.196  22.418  1.00164.98           C
ATOM   6184  C4'  DT I -72     -45.310 -34.425  20.919  1.00164.44           C
ATOM   6185  O4'  DT I -72     -45.104 -33.169  20.226  1.00164.50           O
ATOM   6186  C3'  DT I -72     -44.176 -35.341  20.471  1.00164.05           C
ATOM   6187  O3'  DT I -72     -44.756 -36.505  19.899  1.00163.49           O
ATOM   6188  C2'  DT I -72     -43.369 -34.526  19.455  1.00164.06           C
ATOM   6189  C1'  DT I -72     -44.333 -33.408  19.066  1.00164.11           C


Best,
Shuxiang

12
Web DSSR is a user-friendly web-based interface for analyzing and visualizing three-dimensional (3D) nucleic-acid-containing structures. The server allows the user to determine a wide variety of conformational parameters in a given PDB ID or uploaded structure. Meanwhile, the secondary structure visualization component offers simultaneously highlighting of 1D, 2D, and 3D nucleic-acid structures.

The wDSSR web server is located at http://web.x3dna-dssr.org/.

Any questions and bug reports are welcome!


13
Dear Xiangjun,

I used DSSR-enhanced visualization web server to display ribosome structures such as 5afi, 5j4b. All my tried failed. I'm not sure it is my browser problem or the web server inner error. Thank you.

Best,
Shuxiang   

14
Dear Xiangjun,

I tried to use the following dbn file generated by DSSR and display its RNA secondary structure in forna (a RNA secondary structure visualization tool). However, it looks like forna doesn't recognize multiple sequences and "&" notation. It there a way to get around this? Thank you.

>2F4V nts=1511 [2F4V] -- secondary structure derived by DSSR
UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGG&CCGCGGGGUUUU&ACUCCG&UGGUC&AGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUU&GCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAA&CCCGGGACGAAACCCCCGACGA&GGGGACUGACGGUACCGGG&GUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCU&CCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGG&AGCCUACGGG&CAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUC&A&UUCU
....((((..[.[[[..)))).((((.(((((..(((((((((....(((.(((..(((..((.((&((((((((....&.)))))&)))))&.)))))......(((......((((((((..((...(((((((.(((((....((((((....)))))).....)))))....((((.(((((....))))).))))...((((...&)))).)))))))..))))))))))(((....(((..((((((((.......)))))))))))......)))..((((((((....))))...))))))).(((((............))))).((((....))))...)))))).).....(.(((...((.((....)).).))))).)).))))))..((((.......(((....)))......))))....&(.(((...(....((((.....&)))).....)....))).)&......((((([[[...(((((.....((.]]])).......))))))))))..)))))))))..........((([[...(.((((...(((.(((((((.((((((((((......((((((.....))))))....))))))))..)))))))))..(((.(((((...((((((((...(((((((....((........)).......)))))))...).......((....)).)))))))..)))))..))..))))...))))....((((((...((...((((.........))))...))))))))......{...((((((..((((((((((...&))))))))))...((..]])).....)))))))))).(((......((((....))))....)))...]]].](((((.(((((((.((..(((((..((((((((((......((........))..........((((((...(...((............(.(....).)........(((....).))........))).((.(((...((((((.(....(((((((((....)))..((((......))))..)))))).....((((.(((((.....(....(.......)..)......)))))..(..(((((....))))).....)..)))).....).).)))...)).))))).....))))))..[)).)))))))).(...(((((((.....(((..((..((((....))))..))....))).....)))))))......(....(((((((........)))))))....)..)..))))).....(((((((......]...)))))))......))...)))))))))).))..(.(..((.(.((((.(((..((.(((.((((((...(.((((...&.(((....))&).)))).)..)))))).))).))..))).))))..).))...)..)..(((((((((....)))))))))}....&.&....

Best,
Shuxiang                                                           


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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.