15  structures 0  species 0  sequences

Motif: sarcin-ricin-2 (RM00019)

Description: Sarcin-ricin motif 2

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 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 3IZ9 A 71 - 112
2 3IZF A 72 - 113
2 1J5A A 205 - 246
2 2zkr 0 57 - 98
2 2HGH B 12 - 55
2 1yhq 9 64 - 117
2 3zvp A 479 - 502
2 3pip X 214 - 237
2 3bbo A 222 - 245
2 3DIL A 21 - 70
2 2AW4 B 2645 - 2674
2 1J5E A 1325 - 1361
2 1s72 0 197 - 239
2 1un6 F 14 - 60
2 2j01 A 215 - 256

Family matches

There are 4 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 RF00168 Lysine riboswitch 37 0.787 853.8 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 70 0.769 1784.8 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 97 0.951 2188.6 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 72 0.818 1507.2 Match Image

References

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

Literature references

  1. Leontis NB, Westhof E J. Mol. Biol. 1998;283:571–583. A common motif organizes the structure of multi‐helix loops in 16 S and 23 S ribosomal RNAs. PUBMED:9784367

  2. Duarte CM, Wadley LM, Pyle AM Nucleic Acids Res. 2003;31:4755-4761. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. PUBMED:12907716

  3. 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

  4. Cruz JA, Westhof E Nat Methods. 2011;8:513-21. Sequence-based identification of 3D structural modules in RNA with RMDetect. PUBMED:21552257

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:9784367
Structure source N/A
Type Internal Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 56 55.34 42

Model information

Build commands
cmbuild -F sarcin-ricin-CM sarcin-ricin-SEED
cmcalibrate --mpi --seed 1 sarcin-ricin-CM
Gathering cutoff 15.0
Covariance model Download the Infernal CM for the motif here