12  structures 0  species 0  sequences

Motif: k-turn-2 (RM00011)

Description: Kink turn 2, 5' bulge


Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled Internal loop. More...

Internal-loops (also termed interior loops) in RNA are found where the double stranded RNA separates due to no Watson-Crick base pairing between the nucleotides. Internal-loops differ from Stem-loops as they occur in middle of a stretch of double stranded RNA. The non-canonicoal residues result in the double helix becoming distorted due to unwinding, unstacking and kinking.

Internal-loops can be classified as either symmetrical or asymmetrical, with some asymmetrical internal-loops, also known as bulges. Many important structural motifs are composed of internal loops such as the C-loop,[1] the docking-elbow,[2] kink-turns (k-turn),[3][4] the right-angle,[5] the sarcin/ricin loops (also called bulged-G motifs),[6][7][8] the twist-up motif[9] and the UAA/GAN internal loop motif.[10]


  1. ^ Lescoute, A; Leontis, NB; Massire, C; Westhof, E (2005). "Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments". Nucleic Acids Research. 33 (8): 2395–409. doi:10.1093/nar/gki535. PMC 1087784. PMID 15860776.
  2. ^ Lehmann, J; Jossinet, F; Gautheret, D (May 1, 2013). "A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders". Nucleic Acids Research. 41 (10): 5494–502. doi:10.1093/nar/gkt219. PMC 3664808. PMID 23580544.
  3. ^ Klein, D.J. (2001). "The kink-turn: a new RNA secondary structure motif". The EMBO Journal. 20 (15): 4214–4221. doi:10.1093/emboj/20.15.4214. ISSN 1460-2075. PMC 149158.
  4. ^ Schroeder, KT; McPhee, SA; Ouellet, J; Lilley, DM (Aug 2010). "A structural database for k-turn motifs in RNA". RNA. 16 (8): 1463–8. doi:10.1261/rna.2207910. PMC 2905746. PMID 20562215.
  5. ^ Grabow, WW; Zhuang, Z; Swank, ZN; Shea, JE; Jaeger, L (Nov 23, 2012). "The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns". Journal of Molecular Biology. 424 (1–2): 54–67. doi:10.1016/j.jmb.2012.09.012. PMC 3488136. PMID 22999957.
  6. ^ a b c Szewczak, AA; Moore, PB (Mar 17, 1995). "The sarcin/ricin loop, a modular RNA". Journal of Molecular Biology. 247 (1): 81–98. doi:10.1006/jmbi.1994.0124. PMID 7897662.
  7. ^ Leontis, NB; Westhof, E (Oct 30, 1998). "A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs". Journal of Molecular Biology. 283 (3): 571–83. doi:10.1006/jmbi.1998.2106. PMID 9784367.
  8. ^ Moore PB (1999). "Structural motifs in RNA". Annu. Rev. Biochem. 68: 287–300. doi:10.1146/annurev.biochem.68.1.287. PMID 10872451.
  9. ^ a b Zhong, C; Zhang, S (Feb 2012). "Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment". Nucleic Acids Research. 40 (3): 1307–17. doi:10.1093/nar/gkr804. PMC 3273805. PMID 21976732.
  10. ^ a b Lee, JC; Gutell, RR; Russell, R (Jul 28, 2006). "The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions". Journal of Molecular Biology. 360 (5): 978–88. doi:10.1016/j.jmb.2006.05.066. PMID 16828489.

See also

This page is based on a wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.


You can either download the motif alignment or view it directly in your browser window. More...

Formatting options

You can view or download motif alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Alignment format:


There are 12 PDB entires which have been used to build the motif model.

The table of results below may be sorted by clicking on the column titles, or restored to the original order here.

Original order PDB ID PDB chain ID PDB Residues
2 1FFK 0 1303 - 1352
2 2GYA 0 1122 - 1175
2 1vsa w 1221 - 1276
2 1C2W B 2125 - 2162
2 3JYX 5 1338 - 1387
2 1giy A 1244 - 1298
2 1J5A A 2102 - 2161
2 2aw4 B 1197 - 1252
2 1s72 0 1305 - 1352
2 1e7k C 1 - 22
2 3cc2 0 1136 - 1215
2 2wh2 A 2134 - 2168

Family matches

There are 3 Rfam families which match this motif.

This section shows the families which have been annotated with this motif. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order Family Accession Family Description Number of Hits Fraction of Hits Sum of Bits Image
3 RF02540 Archaeal large subunit ribosomal RNA 91 1.000 5908.2 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 99 0.971 4618.3 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 30 0.341 682.0 Match Image


This section shows the database cross-references that we have for this Rfam motif.

Literature references

  1. Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB J Math Biol. 2008;56:215-52. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. PUBMED:17694311

  2. Klosterman PS, Hendrix DK, Tamura M, Holbrook SR, Brenner SE Nucleic Acids Res. 2004;32:2342-52. Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. PUBMED:15121895

  3. Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB Nucleic Acids Res. 2009;37:4898-918. Classification and energetics of the base-phosphate interactions in RNA. PUBMED:19528080

  4. Schroeder KT, McPhee SA, Ouellet J, Lilley DM RNA. 2010;16:1463-8. A structural database for k-turn motifs in RNA. PUBMED:20562215

  5. Blouin S, Chinnappan R, Lafontaine DA Nucleic Acids Res. 2010 Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation. PUBMED:21169337

  6. Meyer M, Westhof E, Masquida B RNA Biol. 2012;9:[Epub ahead of print]. A structural module in RNase P expands the variety of RNA kinks. PUBMED:22336704

  7. Lescoute A, Leontis NB, Massire C, Westhof E Nucleic Acids Res. 2005;33:2395-409. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments. PUBMED:15860776

External database links

Curation and motif details

This section shows the detailed information about the Rfam motif. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.


Seed source Published; PMID:19528080
Structure source N/A
Type Internal Loop
Author Gardner PP
Alignment details
Alignment Number of
Average length Sequence
identity (%)
seed 14 50.43 43

Model information

Build commands
cmbuild -F k-turn-CM k-turn-SEED
cmcalibrate --mpi --seed 1 k-turn-CM
Gathering cutoff 18.0
Covariance model Download the Infernal CM for the motif here