Limits...
The 3D rRNA modification maps database: with interactive tools for ribosome analysis.

Piekna-Przybylska D, Decatur WA, Fournier MJ - Nucleic Acids Res. (2007)

Bottom Line: Additionally, the database integrates information about positions of modifications within rRNA sequences and secondary structures, as well as links to other databases and resources about modifications and their biosynthesis.A section called 'Paint Your Own' enables the user to create a 3D modification map for rRNA from any organism where sites of modification are known.This section also provides capabilities for visualizing nucleotides of interest in rRNA or tRNA, as well as particular amino acids in ribosomal proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.

ABSTRACT
The 3D rRNA modification maps database is the first general resource of information about the locations of modified nucleotides within the 3D structure of the full ribosome, with mRNA and tRNAs in the A-, P- and E-sites. The database supports analyses for several model organisms, including higher eukaryotes, and enables users to construct 3D maps for other organisms. Data are provided for human and plant (Arabidopsis) ribosomes, and for other representative organisms from eubacteria, archaea and eukarya. Additionally, the database integrates information about positions of modifications within rRNA sequences and secondary structures, as well as links to other databases and resources about modifications and their biosynthesis. Displaying positions of modified nucleotides is fully manageable. Views of each modified nucleotide are controlled by individual buttons and buttons also control the visibility of different ribosomal molecular components. A section called 'Paint Your Own' enables the user to create a 3D modification map for rRNA from any organism where sites of modification are known. This section also provides capabilities for visualizing nucleotides of interest in rRNA or tRNA, as well as particular amino acids in ribosomal proteins. The database can be accessed at http://people.biochem.umass.edu/fournierlab/3dmodmap/

Show MeSH
Paint Your Own. Users may create 3D modification maps for rRNA from any organism. The ‘Paint Your Own’ section with an accompanying tutorial enables selection and highlighting of any site or segment within an rRNA, r-protein and tRNA. The example shown is for a deduced 3D arrangement of predicted 2′-O-methylations concentrated within the GTPase center of P. abyssi, using the ribosome model at 5.5 Å. Stepwise, visualization was achieved by: (i) determining the equivalent numbers of the rRNA nucleotides from the secondary structure of E. coli 23S rRNA (53) and, (ii) selecting and highlighting the GTPase center and the positions of the modified nucleotides, using a few commands provided in the Jmol console window. The rRNA fragment of the GTPase center is shown as a thick white backbone, and modified nucleotides are displayed as green dots. The tRNAs are placed in the A- (pink), P- (purple) and E- (cyan) sites of the LSU. A fragment of mRNA within the small ribosomal subunit (hidden) is displayed in yellow. Proteins of the LSU are also hidden.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238946&req=5

Figure 2: Paint Your Own. Users may create 3D modification maps for rRNA from any organism. The ‘Paint Your Own’ section with an accompanying tutorial enables selection and highlighting of any site or segment within an rRNA, r-protein and tRNA. The example shown is for a deduced 3D arrangement of predicted 2′-O-methylations concentrated within the GTPase center of P. abyssi, using the ribosome model at 5.5 Å. Stepwise, visualization was achieved by: (i) determining the equivalent numbers of the rRNA nucleotides from the secondary structure of E. coli 23S rRNA (53) and, (ii) selecting and highlighting the GTPase center and the positions of the modified nucleotides, using a few commands provided in the Jmol console window. The rRNA fragment of the GTPase center is shown as a thick white backbone, and modified nucleotides are displayed as green dots. The tRNAs are placed in the A- (pink), P- (purple) and E- (cyan) sites of the LSU. A fragment of mRNA within the small ribosomal subunit (hidden) is displayed in yellow. Proteins of the LSU are also hidden.

Mentions: While our database is designed for visualizing modified ribosomal nucleotides of human, Arabidopsis, S. cerevisiae, H. marismortui, E. coli and T. thermophilus, it is not limited to 3D modification maps for these organisms. The user can also ‘paint’ or specifically highlight positions of modifications (or other sites) in rRNAs of other species as well, as permitted by the sequence and modification data available. A section ‘Paint Your Own’ shows users how to create their own 3D modification map using the Jmol console (Figure 2). We lead the user to pages with codes of ribosomal molecules for both 70S models, and describe how to display desired portions of the ribosome in various formats using the appropriate commands.Figure 2.


The 3D rRNA modification maps database: with interactive tools for ribosome analysis.

Piekna-Przybylska D, Decatur WA, Fournier MJ - Nucleic Acids Res. (2007)

Paint Your Own. Users may create 3D modification maps for rRNA from any organism. The ‘Paint Your Own’ section with an accompanying tutorial enables selection and highlighting of any site or segment within an rRNA, r-protein and tRNA. The example shown is for a deduced 3D arrangement of predicted 2′-O-methylations concentrated within the GTPase center of P. abyssi, using the ribosome model at 5.5 Å. Stepwise, visualization was achieved by: (i) determining the equivalent numbers of the rRNA nucleotides from the secondary structure of E. coli 23S rRNA (53) and, (ii) selecting and highlighting the GTPase center and the positions of the modified nucleotides, using a few commands provided in the Jmol console window. The rRNA fragment of the GTPase center is shown as a thick white backbone, and modified nucleotides are displayed as green dots. The tRNAs are placed in the A- (pink), P- (purple) and E- (cyan) sites of the LSU. A fragment of mRNA within the small ribosomal subunit (hidden) is displayed in yellow. Proteins of the LSU are also hidden.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238946&req=5

Figure 2: Paint Your Own. Users may create 3D modification maps for rRNA from any organism. The ‘Paint Your Own’ section with an accompanying tutorial enables selection and highlighting of any site or segment within an rRNA, r-protein and tRNA. The example shown is for a deduced 3D arrangement of predicted 2′-O-methylations concentrated within the GTPase center of P. abyssi, using the ribosome model at 5.5 Å. Stepwise, visualization was achieved by: (i) determining the equivalent numbers of the rRNA nucleotides from the secondary structure of E. coli 23S rRNA (53) and, (ii) selecting and highlighting the GTPase center and the positions of the modified nucleotides, using a few commands provided in the Jmol console window. The rRNA fragment of the GTPase center is shown as a thick white backbone, and modified nucleotides are displayed as green dots. The tRNAs are placed in the A- (pink), P- (purple) and E- (cyan) sites of the LSU. A fragment of mRNA within the small ribosomal subunit (hidden) is displayed in yellow. Proteins of the LSU are also hidden.
Mentions: While our database is designed for visualizing modified ribosomal nucleotides of human, Arabidopsis, S. cerevisiae, H. marismortui, E. coli and T. thermophilus, it is not limited to 3D modification maps for these organisms. The user can also ‘paint’ or specifically highlight positions of modifications (or other sites) in rRNAs of other species as well, as permitted by the sequence and modification data available. A section ‘Paint Your Own’ shows users how to create their own 3D modification map using the Jmol console (Figure 2). We lead the user to pages with codes of ribosomal molecules for both 70S models, and describe how to display desired portions of the ribosome in various formats using the appropriate commands.Figure 2.

Bottom Line: Additionally, the database integrates information about positions of modifications within rRNA sequences and secondary structures, as well as links to other databases and resources about modifications and their biosynthesis.A section called 'Paint Your Own' enables the user to create a 3D modification map for rRNA from any organism where sites of modification are known.This section also provides capabilities for visualizing nucleotides of interest in rRNA or tRNA, as well as particular amino acids in ribosomal proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA.

ABSTRACT
The 3D rRNA modification maps database is the first general resource of information about the locations of modified nucleotides within the 3D structure of the full ribosome, with mRNA and tRNAs in the A-, P- and E-sites. The database supports analyses for several model organisms, including higher eukaryotes, and enables users to construct 3D maps for other organisms. Data are provided for human and plant (Arabidopsis) ribosomes, and for other representative organisms from eubacteria, archaea and eukarya. Additionally, the database integrates information about positions of modifications within rRNA sequences and secondary structures, as well as links to other databases and resources about modifications and their biosynthesis. Displaying positions of modified nucleotides is fully manageable. Views of each modified nucleotide are controlled by individual buttons and buttons also control the visibility of different ribosomal molecular components. A section called 'Paint Your Own' enables the user to create a 3D modification map for rRNA from any organism where sites of modification are known. This section also provides capabilities for visualizing nucleotides of interest in rRNA or tRNA, as well as particular amino acids in ribosomal proteins. The database can be accessed at http://people.biochem.umass.edu/fournierlab/3dmodmap/

Show MeSH