15  structures 0  species 0  sequences

Motif: ANYA (RM00001)

Description: ANYA tetraloop

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 Tetraloop 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 15 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 1D0T A 1 - 21
2 1RHT A 1 - 24
2 17RA A 1 - 20
2 2C51 R 1 - 19
2 1aq3 R -
2 1zdk R -
2 1zdh R -
2 1zdj R -
2 2iz8 R -
2 2izn R -
2 2c4z R -
2 2iz9 R -
2 2c4y R -
2 2c50 R -
2 2izm R -

Family matches

There is 1 Rfam family which matches 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 RF02359 Bacteriophage MS2 operator hairpin 5 1.000 141.5 Match Image

References

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

Literature references

  1. Convery MA, Rowsell S, Stonehouse NJ, Ellington AD, Hirao I, Murray JB, Peabody DS, Phillips SE, Stockley PG Nat Struct Biol. 1998;5:133–139. Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution. PUBMED:9461079

  2. Rowsell S, Stonehouse NJ, Convery MA, Adams CJ, Ellington AD, Hirao I, Peabody DS, Stockley PG, Phillips SE. Nat Struct Biol. 1998;5(11):970-975. Crystal structures of a series of RNA aptamers complexed to the same protein target. PUBMED:9808042

  3. 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

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 Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 15 18.87 75

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 20.0
Covariance model Download the Infernal CM for the motif here