Last modified on 09 October 2002.

Literature Reference:

Jackson S.A., Cannone J.J., Lee J.C., Gutell R.R., and Woodson S.A. (2002)
Distribution of rRNA Introns in the Three-Dimensional Structure of the Ribosome.
Running Title: rRNA Introns in 3D.
Journal of Molecular Biology, 323:35-52.

Manuscript Figures and Tables:

Figure/Table Legend Panel
A B Composite
Table 1. Number of known intron sequences at each intron position. 16S rRNA ( HTML ) 23S rRNA ( HTML )  
Table 2. Conservation of rRNA residues prior to intron insertion sites. ( HTML ) Number of intron-containing positions adjacent to highly conserved rRNA residues. ( HTML )  
Figure 1. Distribution of introns in rRNAs. 16S rRNA ( JPG ) 23S rRNA ( JPG )  
Figure 2. Location of introns in 16S rRNAs. Secondary structure ( PS | PDF ) Three-dimensional structure of 30S ribosome ( PDF | TIFF )  
Figure 3. Location of introns in 23S rRNAs. Secondary structure ( PS | PDF ) Three-dimensional structure of 50S ribosome ( PDF | TIFF )  
Figure 4. Three-dimensional clustering of rRNA intron sites within 70 S ribosome. Comparison of rRNA positions ( JPG ) Comparison of intron types ( JPG )  
Figure 5. Conservation of rRNAs. 30S (front view) ( TIFF ) 50S (crown view) ( TIFF ) Composite ( PDF | TIFF )
Figure 6. Proximity of intron sites to tRNA bound in the 70S ribosome. Figure 6 ( JPG )
Figure 7. Surface accessibility of intron positions in mature ribosomal subunits. 16S Introns ( JPG ) 23S Introns ( JPG )  
Figure 8. Locations of reverse splicing targets in E. coli 23S rRNA. Crown view ( TIFF ) Back view ( TIFF ) Composite ( PDF | TIFF )

Additional Figures and Tables:

Secondary Structure Diagrams and RasMol Scripts Showing Intron Positions (from 14 February 2002 data):

Dimensions in Data Presentation: A, intron types (i.e., group I, group II, archaeal, spliceosomal, and unknown); B, the number of introns per site (for 3D images only); C, rRNA sites within 10.0 Å of tRNA/mRNA; D, extent of conservation of the 16S and 23S rRNAs; E, structural domains from the 16S and 23S rRNA secondary structure models are distinguished.

Structure Diagrams: Secondary structure and conservation diagrams use Escherichia coli as a reference sequence. Intron position diagrams were last updated in February 2002. File formats: PS = PostScript; PDF = Adobe Portable Document Format.

RasMol Scripts: Frequency-Dependent Sphere Sizes for Intron Positions: large, intron positions with more than 10% of the total introns; medium, intron positions with 1-10% of the total introns; small, intron positions with less than 1% of the total introns. Color codes for conserved nucleotides (positions that are present in at least 95% of the sequences): red, 98-100% conserved nucleotides; green, 90-98% conserved nucleotides; blue, 80-90% conserved nucleotides; yellow, less than 80% conserved nucleotides; gray, "arc" regions from conservation diagrams (positions which are present in less than 95% of the sequences). Thicker lines show nucleotides within 10.0 Å of the APE-tRNAs and mRNA.
Contents Exon
16S rRNA 30S ribosome (1FJF) 23S rRNA (5' half) 23S rRNA (3' half) 50S ribosome (1JJ2) 16S + 23S + tRNA/70S + tRNA (1GIX + 1GIY)
1) Intron Positions on the Escherichia coli IISTR:
Dimensions: A, B, C
PS | PDF 16S | 30S PS | PDF PS | PDF 23S | 50S 16S + 23S + tRNAs | 70S + tRNAs
2A) Intron Positions on the Three Phylogenetic Domains Conservation Diagram
Dimensions: A, B, C, D
PS | PDF 16S PS | PDF PS | PDF 23S  
2B) Intron Positions on the Three Phylogenetic Domains/Two Organelles Conservation Diagram
(Starting Point for Figures 2A and 3A)
Dimensions: A, B, C, D
PS | PDF 16S PS | PDF PS | PDF 23S  
3) Intron Positions and Color-Coded rRNA Domains
Dimensions: B, E
PS | PDF 16S | 30S PS | PDF PS | PDF 23S | 50S  
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Conservation and Intron Distribution Information:

Conservation class abbreviations: A, nt present in at least 95% of sequences and is 98-100% conserved; B, nt present in at least 95% of sequences and is 90-98% conserved; C, nt present in at least 95% of sequences and is 80-90% conserved; D, nt present in at least 95% of sequences and is less than 80% conserved; N, nt present in less than 95% of sequences.

Conservation data abbreviations: 3P, Three Phylogenetic Domains; 3P2O, Three Phylogenetic Domains/Two Organelles.

For the tables which are present in two versions: Manuscript, data version used in the preparation of the manuscript; Current, current version of the data (updated daily).
  16S rRNA 23S rRNA
Conservation Data 3P | 3P2O (Text) 3P | 3P2O (Text)
Source Data for Table 1: Table 1A: Manuscript | Current Table 1B: Manuscript | Current
Source Data for Tables 2a and 2b: Manuscript: Full | Summary
Current: Full | Summary
Online Table. Spatial clustering of intron insertion sites within the ribosome (Å). ( HTML )
rRNA Introns Data (CRW Site) Tables of intron data sorted by various criteria. ( HTML )