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. More...
This page is based on a wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
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".
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 |
|
| 3 | RF02541 | Bacterial large subunit ribosomal RNA | 99 | 0.971 | 4618.3 |
|
| 3 | RF02543 | Eukaryotic large subunit ribosomal RNA | 30 | 0.341 | 682.0 |
|
References
This section shows the database cross-references that we have for this Rfam motif.
Literature references
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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
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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
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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
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Schroeder KT, McPhee SA, Ouellet J, Lilley DM RNA. 2010;16:1463-8. A structural database for k-turn motifs in RNA. PUBMED:20562215
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Blouin S, Chinnappan R, Lafontaine DA Nucleic Acids Res. 2010 Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation. PUBMED:21169337
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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
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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 |
|
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 |
