12  structures 0  species 0  sequences

Motif: k-turn-2 (RM00011)

Description: Kink turn 2, 5' bulge

Summary

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 but we are unable to retrieve the article content at this time. More...

Alignments

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:
Download/view:

Structures

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

References

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.

Curation

Seed source Published; PMID:19528080
Structure source N/A
Type Internal Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
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