Recent Posts

21

RNA structures (DSSR) / create a multiple copy from a building block with DSSR-pro

« Last post by amirtaghavi on January 28, 2022, 11:23:34 am »

Hello Dr. Lu,

I am using the DSSR-pro and the work flow you provided to create a multiple copy of a 3bp RNA (attached), I was wondering if it is possible to use the DSSR to create the lost backbone connections.

Thanks,
Amir

x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb

x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair -o=ref-conn.pdb

x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb' -o=temp1.pdb

x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair -o=temp2.pdb
x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb

x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb' -o=duplicate-model.pdb

22

Site announcements / DSSR-enabled innovative PyMOL schematics in the covers of the RNA Journal

« Last post by xiangjun on December 20, 2021, 11:31:10 am »

The DSSR-PyMOL schematics have been featured in all 12 cover images (January to December) of the RNA Journal in 2021. Moreover, the January 2022 issue of RNA continues to highlight DSSR-enabled schematics (see the note below). In the current Covid-19 pandemic, this cover seems to be a fit for the upcoming Christmas holiday season.

Ebola virus matrix protein octameric ring (PDB id: 7K5L; Landeras-Bueno S, Wasserman H, Oliveira G, VanAernum ZL, Busch F, Salie ZL, Wysocki VH, Andersen K, Saphire EO. 2021. Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form. Cell Rep 35: 108986). The Ebola virus matrix protein (VP40) forms distinct structures linked to distinct functions in the virus life cycle. VP40 forms an octameric ring-shaped (D4 symmetry) assembly upon binding of RNA and is associated with transcriptional control. RNA backbone is displayed as a red ribbon; block bases use NDB colors: A—red, G—green, U—cyan; protein is displayed as a gold ribbon. Cover image provided by the Nucleic Acid Database (ndbserver.rutgers.edu). Image generated using DSSR and PyMOL (Lu XJ. 2020. _Nucleic Acids Res_ *48*: e74).

Thanks to Dr. Cathy Lawson at the NDB for generating these cover images using DSSR and PyMOL for the RNA Journal. I'm gratified that the 2020 NAR paper is explicitly acknowledged: it's the first time I've published as a single author in my scientific career.

Did you know that you can easily generate similar DSSR-PyMOL schematics via the http://skmatic.x3dna.org/ website? It is "simple and effective", "good for teaching", and has been highly recommended by Dr. Quentin Vicens (CU Denver) in FacultyOpinions.com.


The 12 PDB structures illustrated in the 2021 covers are:

• January 2021 "iMango-III fluorescent aptamer (PDB id: 6PQ7; Trachman III RJ, Stagno JR, Conrad C, Jones CP, Fischer P, Meents A, Wang YX, Ferre-D'Amare AR. 2019. Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser. Acta Cryst F 75: 547). Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold)."
• February 2021 "Human adenosine deaminase (E488Q mutant) acting on dsRNA (PDB id: 6VFF; Thuy-Boun AS, Thomas JM, Grajo HL, Palumbo CM, Park S, Nguyen LT, Fisher AJ, Beal PA. 2020. Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition. Nucleic Acids Res. https://doi.org/10.1093/nar/gkaa532). Adenosine deaminase enzymes convert adenosine to inosine in duplex RNA, a modification that strongly affects RNA structure and function in multiple ways."
• March 2021 "Hepatitis A virus IRES domain V in complex with Fab (PDB id: 6MWN; Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. 2019. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun 10: 3629)."
• April 2021 "Mouse endonuclease V in complex with 23mer RNA (PDB id: 6OZO; Wu J, Samara NL, Kuraoka I, Yang W. 2019. Evolution of inosine-specific endonuclease V from bacterial DNase to eukaryotic RNase. Mol Cell 76: 44). Endonuclease V cleaves the second phosphodiester bond 3′ to a deaminated adenosine (inosine). Although highly conserved, EndoV change substrate preference from DNA in bacteria to RNA in eukaryotes."
• May 2021 "Manganese riboswitch from Xanthmonas oryzae (PDB id: 6N2V; Suddala KC, Price IR, Dandpat SS, Janeček M, Kührová P, Šponer J, Banáš P, Ke A, Walter NG. 2019. Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch. Nat Commun 10: 4304). Bacterial manganese riboswitches control the expression of Mn2+ homeostasis genes. Using FRET, it was shown that an extended 4-way-junction samples transient docked states in the presence of Mg2+ but can only dock stably upon addition of submillimolar Mn2+."
• June 2021 "Sulfolobus islandicus Csx1 RNase in complex with cyclic RNA activator (PDB id: 6R9R; Molina R, Stella S, Feng M, Sofos N, Jauniskis V, Pozdnyakova I, Lopez-Mendez B, She Q, Montoya G. 2019. Structure of Csx1-cOA4 complex reveals the basis of RNA decay in Type III-B CRISPR-Cas. Nat Commun 10: 4302). CRISPR-Cas multisubunit complexes cleave ssRNA and ssDNA, promoting the generation of cyclic oligoadenylate (cOA), which activates associated CRISPR-Cas RNases. The Csx1 RNase dimer is shown with cyclic (A4) RNA bound."
• July 2021 "M. tuberculosis ileS T-box riboswitch in complex with tRNA (PDB id: 6UFG; Battaglia RA, Grigg JC, Ke A. 2019. Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators. Nat Struct Mol Biol 26: 1106). T-box riboregulators are a class of cis-regulatory RNAs that govern the bacterial response to amino acid starvation by binding, decoding, and reading the aminoacylation status of specific transfer RNAs."
• August 2021 "CAG repeats recognized by cyclic mismatch binding ligand (PDB id: 6QIV; Mukherjee S, Blaszczyk L, Rypniewski W, Falschlunger C, Micura R, Murata A, Dohno C, Nakatan K, Kiliszek A. 2019. Structural insights into synthetic ligands targeting A–A pairs in disease-related CAG RNA repeats. Nucleic Acids Res 47:10906). A large number of hereditary neurodegenerative human diseases are associated with abnormal expansion of repeated sequences. RNA containing CAG repeats can be recognized by synthetic cyclic mismatch-binding ligands such as the structure shown."
• September 2021 "Corn aptamer complex with fluorophore Thioflavin T (PDB id: 6E81; Sjekloca L, Ferre-D'Amare AR. 2019. Binding between G quadruplexes at the homodimer interface of the Corn RNA aptamer strongly activates Thioflavin T fluorescence. Cell Chem Biol 26: 1159). The fluorescent compound Thioflavin T, widely used for the detection of amyloids, is bound at the dimer interface of the homodimeric G-quadruplex-containing RNA Corn aptamer."
• October 2021 "Cas9 nuclease-sgRNA complex with anti-CRISPR protein inhibitor (PDB id: 6JE9; Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, et al. 2019. Structures of Neisseria meningitidis Cas9 complexes in catalytically poised and anti-CRISPR-inhibited states. Mol Cell 76: 938­–952.e5). Nme1Cas9, a compact nuclease for in vivo genome editing. AcrIIC3 is an anti-CRISPR protein inhibitor."
• November 2021 "Two-quartet RNA parallel G-quadruplex complexed with porphyrin (PDB id: 6JJI; Zhang Y, Omari KE, Duman R, Liu S, Haider S, Wagner A, Parkinson GN, Wei D. 2020. Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths. Nucleic Acids Res 48: 9886–9898)."
• December 2021 "Structure of S. pombe Lsm1–7 with RNA, polyuridine with 3' guanosine (PDB id: 6PPV; Montemayor EJ, Virta JM, Hayes SM, Nomura Y, Brow DA, Butcher SE. 2020. Molecular basis for the distinct cellular functions of the Lsm1–7 and Lsm2–8 complexes. RNA 26: 1400–1413). Eukaryotes possess eight highly conserved Lsm (like Sm) proteins that assemble into circular, heteroheptameric complexes, bind RNA, and direct a diverse range of biological processes. Among the many essential functions of Lsm proteins, the cytoplasmic Lsm1–7 complex initiates mRNA decay, while the nuclear Lsm2–8 complex acts as a chaperone for U6 spliceosomal RNA."

23

Site announcements / BioExcel webinar on DSSR

« Last post by xiangjun on November 23, 2021, 11:38:53 am »

On December 9, 2021, at 15:00 CET, I will present a BioExcel webinar titled "X3DNA-DSSR, a resource for structural bioinformatics of nucleic acids."

• The announcement is available here: https://bioexcel.eu/webinar-x3dna-dssr-a-resource-for-structural-bioinformatics-of-nucleic-acids-2021-12-09/.
• Here is the registration URL: https://us02web.zoom.us/webinar/register/WN_g55wmd9ETmeQwQuLfjH57g.

For the record, the screenshot of the announcement is shown below:

24

General discussions (Q&As) / installation error in MAC

« Last post by dnalectronics on November 22, 2021, 02:16:43 pm »

I tried to install x3DNA in mac and it shows "-bash: final_pair:command not found".
I went to bin and clicked on x3dna set up and it showed that I need to copy export X3DNA and PATH to ~./bashrc file. I went to terminal and created a bashrc file and copied the above things. Now I tried to run source ~/.bashrc, I think it was successful but when I typed final_pair -h it shows error. Can you please help me in solving this error?

Thank you!

25

Site announcements / No more grant funding for 3DNA/DSSR

« Last post by xiangjun on October 30, 2021, 09:58:15 pm »

Due to a lack of governmental funding support, we are no longer able to provide DSSR free of charge to the community. Academic users may submit a license request for DSSR Basic or DSSR Pro by clicking "Express Licensing". Commercial users may inquire about pricing and licensing terms by emailing techtransfer@columbia.edu, copying xiangjun@x3dna.org.

DSSR Pro excels in structural bioinformatics of RNA, DNA, and their protein complexes. The software has completely superseded 3DNA, and is being continuously improved. Revenue from licensing supports the development and availability of DSSR.

I am committed to making DSSR a brand that stands for quality and value. By virtue of its unmatched functionality, usability, and support, DSSR would save users a substantial amount of time and effort when compared to competing options.

I designed, implemented, documented, and have continuously improved and supported DSSR. As a result, DSSR users may expect a rapid and concrete answer to their questions. My track record throughout the years has unambiguously demonstrated my dedication to DSSR. I strive to ensure that paying users' trust in DSSR is well-founded by providing them with the best services possible.

As a general rule, the CTV does not provide an evaluation license of DSSR. Potential users should watch the DSSR overview video (20m), browse the Forum, and read DSSR-related papers. If they still have questions or want to see a live demo, I would be pleased to accommodate them. Although more DSSR licenses are definitely beneficial, I do not have the time or desire to directly promote the product, including sending bulk emails to registered users of the Forum. As the developer, I can only strive to make DSSR the best it can be and let the rest sort itself out. I am a strong believer of the old Chinese saying: "酒香不怕巷子深" (Good wine needs no bush).

3DNA is obsolete and no longer maintained or supported. Thanks to the revenue from DSSR licenses, however, the following web-based resources remain accessible to the general public:

• http://web.x3dna.org/ (Web 3DNA 2.0)
• http://skmatic.x3dna.org/ (DSSR-enabled block-view schematics)
• http://G4.x3dna.org/ (DSSR-annotated G-quadruplexes in the PDB)

Additionally, the 3DNA Forum will be maintained so that people can assist one another and archived content would remain accessible. I may chime in occasionally, but I will not be able to continue serving the community for free as I did over the past decade.

26

MD simulations / Re: generate DNA pdb file for Gromacs

« Last post by dnalectronics on October 27, 2021, 01:00:46 pm »

Would you mind explaining to me how did you generate pdb file for your DNA sequence. I am new to this and stuck now on creating pdb file for my MD simulation. I will appreciate any kind of help here.

27

MD simulations / DNA step parameters

« Last post by dnalectronics on October 27, 2021, 09:18:45 am »

I am an experimentalist working on DNA-drug binding. However, to support my result I am trying to do simulation. Since I don't have an experimentally determined structure for my custom 12-mer DNA duplex, I have to create one from scratch. I am using  w3dna.rutgers.edu,  to create a wide variety of nucleic acid structures.  However, I want to know what is base parameter file or where can I get that file.

I will really appreciate if you can please guide me.

Thank you for your help.

28

RNA structures (DSSR) / Re: dssr did not recognize some canonical nucleotide in 6nd4 chain 2

« Last post by xiangjun on October 22, 2021, 05:07:20 pm »

As mentioned in my previous response, DSSR Pro has options to handle such cases, among other features.

DSSR Pro's default output reports 146 nucleotides, along with a diagnostic note for the two deformed bases. Such deformed bases can participate in a variety of loops but not in pairing interactions.

Processing file '6nd42.pdb'
  2.G.248 0.808 -- distorted, without fitted base frame
  2.G.323 0.319 -- distorted, without fitted base frame
    total number of nucleotides: 146

DSSR Pro also has an option that treats those distorted bases as normal for base-pairing interactions.

29

RNA structures (DSSR) / Re: dssr did not recognize some canonical nucleotide in 6nd4 chain 2

« Last post by zcx on October 22, 2021, 02:40:45 pm »

This is probably misleading. For the sake of calculating base pairs, I completely agree that we should not consider nucleobases with highly distorted conformation. However, when counting how many nucleotides are there in the sequence (e.g., when generating ct or dbn files), nucleotides with distorted base conformation (or even nucleotides without their base groups) are still nucleotides. It may not be a good idea to just delete them from the sequence without at least printing out a warning message.

30

RNA structures (DSSR) / Re: dssr did not recognize some canonical nucleotide in 6nd4 chain 2

« Last post by xiangjun on October 21, 2021, 09:47:35 pm »

DSSR is behaving as designed. Please see the section "Identification of nucleotides" of  the 2015 DSSR paper:

A nucleotide is identified if a residue contains at least three base ring atoms and the root-mean-square deviation (rmsd) of the fit falls below a user-definable cutoff. Since base rings are rigid, the rmsd is normally <0.1 Å. To account for experimental error and special non-planar cases, such as 5,6-dihydrouridine (H2U) in yeast tRNA^Phe (Figure 2), the default rmsd cutoff is set to 0.28 Å.

The default DSSR cutoff values are based on extensive tests in real-world applications. Any unidentified nucleotide is almost always due to heavy distortions in its base geometry that is 'beyond recognition'. For example, G248 in your attached 6nd42.pdb file has the PyMOL rendered image as attached. Note the N1-C2 distance is 2.2 Å, far larger than ~1.5 Å (the normal covalent C-N bond length).

DSSR Pro has provisions to handle extreme cases like yours.