Last modified on 15 January 2016.

NOTE: This section is under development.

Literature Reference:

Lee J.C., Cannone J.J., and Gutell R.R.
Three-Dimensional Structure.
Manuscript in preparation.

Basepair Conformations | Structural Motifs | RNA Sequence/Structure Information [RNA2DMap] | Base Stacking | Motif Evolution | RNA-Protein Interaction | RNA 3D Structure Annotation | Help and Legend

1. Basepairs and Their Conformations in RNA Structure

1.A) The Lee-Gutell (LG) System

The Lee-Gutell (LG) system (Lee & Gutell, 2004) was first proposed to systematically describe basepairs and their conformations based on the 10 basepair groups and the topological relationships between two interacing nucleobases and later extended to describe base-backone and backbone-backbone interactions.

1.B) Identification of Basepairs and Their Conformations in RNA-Containing Crystal Structures Using the LG System

1.C) Occurrences of topologically unique base-base, base-backbone, and backbone-backbone interactions in non-redundant natural RNAs

Topologically Unique Base-Base (BB), Base-Backbone(BK), and Backbone-Backbone (KK) Interactions
Basepair Group BB BK KK Sum
C:G 23 28 8 59
U:A 24 21 7 52
U:G 26 29 8 63
G:A 24 38 13 75
C:A 22 20 10 52
U:C 25 11 14 50
A:A 14 9 9 32
C:C 15 4 8 27
G:G 17 17 9 43
U:U 16 6 5 27
Total 206 183 91 480

1.D) Comparison of the Lee-Gutell (LG) System with Other Basepair Nomenclatures to Describe Base-Base Interactions Including:

Comparision of the LG System with Other Basepair Nomenclatures
Nomenclature Comparison 1J5E 1JJ2 1U6B
LG Is the most accurate and reliable nomenclature to identify basepairs and their conformations. Identifies almost no false positive basepairs. 964 1884 122
LW Has no names for those formed through slipping and does not distinguish from sWC from WC and Wb* from Wb. Has no unambiguously defined set of basepair conformations for BK and KK interactions. Basepair conformations are redundantly identified, twice as many as their actual number, based on the 16 basepair types; detected 10874 (1382 basepairs), 20834 (2746 basepairs), and 1578 (218 basepairs) pairwise interactions in 1J5E, 1JJ2, and 1U6B, respectively, composed of basepairs, base stacks, base-backbone contacts, and covalent interactions between adjacent nucleotides (see FR3D). 690

682 (NDB)

1278 (NDB)

100 (NDB)
Olson Has too many redundant names for specific basepair conformations in a basepair group. For example, C:G WC, U:A WC, and G:A S in the LG system can be described by 20, 11, 49 different names, respectively. Has no systematically defined set of basepair conformations for BK and KK interactions. Identifies too many false positives; overall 63% of the total number of 2363 basepair conformations defined by this system are not real. 767 1401 na
Fox Only describes two hydrogen-bonding sites on two interacting nucleotides regardless of their relative spatial orientations and thus has very limited applications to identify various non-canonical basepair conformations. Not applicable
Sanger Has too limited applications to be used to identify basepair conformations. Not applicable

2. Structural Motifs as the Building Blocks of Higher-Order RNA Structure

RNA Structural Motifs References
A platforms Cate et al., 1996
A-minor motifs Doherty et al., 2001; Nissen et al., 2001
AA.AG@helix.ends Elgavish et al., 2001
C loops Lescoute et al., 2005
E loops Wimberly et al., 1993; Leontis & Westhof, 1998
E-like loops Gutell et al., 2000
GAAA receptors Costa & Michel, 1995
H-turns Szep et al., 2003
K-turns Klein et al., 2001
Lonepair triloops Lee et al., 2003; Nagaswamy & Fox, 2002
Tandem G:A internal loops SantaLucia et al., 1990; Gautheret et al., 1994; Walter et al., 1994
Tetraloops Woese et al., 1990
U-turns Quigley & Rich, 1976; Gutell et al., 2000
UAA/GAN, UNA/GAN, and GA/GAA motifs Lee et al., 2006

3. Presentation of RNA Sequence and Structure Information

3.A) RNA2DMap: A tool for online presentation of RNA sequence and structure information using RNA secondary structure diagrams

  • Basepair groups and their conformormations
  • Nucleotide and basepair frequencies
  • Nucleotide conservations
  • Locations of identified structural motifs
  • Coaxial stacking between helices
  • Secondary and tertiary RNA-RNA interactons
  • RNA-RNA distances

3.B) Mapped RNA secondary structure diagrams with crystal structure information

RNA Secondary Structure Diagrams with Crystal Structure Data
Thermus thermophilus 16S rRNA PS | PDF
Haloarcula marismortui 23S rRNA Merged: PS | PDF
5' Half: PS | PDF
3' Half: PS | PDF
Haloarcula marismortui 5S rRNA PS | PDF
Tetrahymena thermophila group I intron RNA PS | PDF
Azoarcus sp. group I intron RNA PS | PDF
Oceanobacillus iheyensis group II intron RNA PS | PDF
Thermatoga maritima RNase P RNA (Type A) PS | PDF
Bacillus subtilus RNase P RNA (Type B) PS | PDF
Bacillus stearothermophilus RNase P RNA (Type B) PS | PDF

4. Quantitative Analysis of Base-Base Stacking

Two nucleotide bases are declared stacked only if all of the three following conditions are satisfied:

  1. The tipping angle between two base planes should be < 25 degrees.
  2. The vertical distance between two base planes should be between 2.7 and 4.1 Angstroms.
  3. At least 15% of the normal vectors from one base plane should pass through the other base plane.
Quantitative Analysis of Base-Base Stacking
Fig. 1. Schematic representation of the three criteria for base-base stacking PDF
Raw text data for base-base stacking in RNA T16S | H23S | H5S | E16S | E23S | E5S | trnF
Data mapped onto RNA secondary structure diagrams (the darker the color, the more the stacking) T16S | H23S | H5S | E16S | E23S | E5S | trnF

5. Evolution of RNA Structural Motifs

The EELL motif is an internal loop motif composed of three evolutionarily closely related RNA structural motifs:

  • AGUA/GAA or E loop motif with the 5'-AGUA/GAA-3' sequence (aka S-turn motif or G-bulge motif)
  • GUA/GAA or E-like (EL) loop motif with the 5'-GUA/GAA-3' sequence (aka E loop motif)
  • GGA/GAA or EL-like (ELL) loop motif with the 5'-GGA/GAA-3' sequence
Evolution between AGUA/GAA (E), GUA/GAA (EL), and GGA/GAA (ELL) Motifs
Fig. 1. Galleries of the EELL motifs occurring in rRNA crystal structure PDF
Fig. 2. Stereoviews for hydrogen-bonding and base-base stacking interactions in the EELL motifs PDF
Fig. 3. Approximate locations of the EELL motifs in rRNA PDF
Tables. Analysis of the EELL motifs in rRNA and their phylogenetic distribution PDF
Viewing EELL motifs identified in crystal structures and their molecular contacts  

6. RNA-Protein Interactions in the Ribosome

RNA-Protein Interactions (RPIs) in the Ribosome
Fig. 1. Sites of H-bonded RPIs on RNA secondary structure diagrams SSU | LSU
Fig. 2. Sites of all RPIs on RNA secondary structure diagrams SSU | LSU
Supplementary data. Sorted text outputs of all RPIs SSU | LSU

7. Annotation of RNA 3D Structure (Ongoing Project)

  1. Create a unique set of structural descriptors for all known RNA structural motifs
  2. Develop a program to read a set of PDB structures and the set of structural descriptor
  3. Identify all known structural motifs and their locations on secondary structure