Home
Database
Research
About us
Elongation factor SelB aptamer
Description
In 1997, Stefanie J. Klug and colleagues used in vitro selection to isolate RNA aptamers that bind to the special elongation factor SelB. SelB-binding variants of the SelB-responsive wild-type fdhF mRNA hairpin, which allow for the dissection of SelB binding from the overall biological function of this mRNA secondary structure. In 1999, Stefanie J. Klug and colleagues used in vitro selection to isolate RNA aptamers that bind to the special elongation factor SelB. They found that the vast majority of aptamers bound to the ultimate C-terminus of SelB, the domain responsible for mRNA hairpin binding[1,2].SELEX
In 1997, Stefanie J. Klug et al. isolated specific sequences with the ability to compete with wild-type fdhF mRNA for SelB binding by four rounds of selection. In 1999, Stefanie J. Klug et al. isolated new variant RNA sequences that bind to SelB with high affinity by four rounds of selection[1,2].
Detailed information are accessible on SELEX page.
Structure
The RNA aptamers all have highly conserved regions that correspond to the apical stem-loop structure of wild-type fdhF mRNA hairpins. The 2D structure of the figures is based on the article by ribodraw tool to draw[2].488 aptamer: 5'-GCCAUAAGUUGUCCCAAGUCUUGGGCGCAAAUACAUCCC-3'
945 aptamer: 5'-GUCACUGACCAUCUGUCGCAGGUCUGCGCACAUCGGUCGUU-3'
|
|
Ligand information
SELEX ligand
SelB (Selenocysteine-specific elongation factor) is a transcription factor necessary for the incorporation of selenocysteine into proteins and binds both transfer RNA (tRNA) and mRNA. This entry represents a domain that adopts a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. In SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit.-----from Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Elongation factor SelB | P14081 | PF09105 | 15.51 kDa | GSPEKILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTLLRVENDLYAISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSF | 2V9V | 948103 |
Affinity of selected RNA molecules for SelB was determined by nitrocellulose filter-binding assays.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| fdhF mRNA | 5'-UGACACGGCCCAUCGGUUGCAGGUCUGCACCAAUCGGUCGGU-3' | SelB protein | 60 nM |
| 488 | 5'-GCCAUAAGUUGUCCCAAGUCUUGGGCGCAAAUACAUCCC-3' | SelB protein | 300 nM |
| 945 | 5'-GUCACUGACCAUCUGUCGCAGGUCUGCGCACAUCGGUCGUU-3' | SelB protein | 120 nM |
Similar compound
We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD(Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.
| PDB | Z-socre | RMSD | Description |
|---|---|---|---|
| 11VA-A | 20.7 | 2.0 | Selenocysteine-specific elongation factor |
| 4ZU9-A | 11.2 | 2.6 | Elongation factor SELB; |
| 8ClI-A | 10.1 | 4.5 | General transcription factor 3c polypertide 1 |
| 7WZE-A | 9.9 | 1.7 | Uncharacterized hth-type transcriptional regulato |
| 6UVU-B | 9.8 | 2.2 | Arsr family transcriptional regulato |
| 6J05-A | 9.8 | 7.9 | Transcriptional regulato Arsr |
| 1SFX-A | 9.7 | 10.2 | Conserved hypothetical protein af2008 |
| 5XPQ-A | 9.7 | 1.6 | Uncharacterized hth-type transcriptional regulato |
| 1KU9-A | 9.7 | 5.6 | Hypothetical protein mj223 |
| 20BP-A | 9.6 | 2.2 | Putative DNA-binding protein |
References
[1] In vitro and in vivo characterization of novel mRNA motifs that bind special elongation factor SelB.Klug, S. J., Hüttenhofer, A., Kromayer, M., & Famulok, M.
Proceedings of the National Academy of Sciences of the United States of America, 94(13), 6676–6681. (1997)
[2] In vitro selection of RNA aptamers that bind special elongation factor SelB, a protein with multiple RNA-binding sites, reveals one major interaction domain at the carboxyl terminus.
Klug, S. J., Hüttenhofer, A., & Famulok, M.
RNA (New York, N.Y.), 5(9), 1180–1190. (1999)