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77 aptamer
Description
Gerard Triqueneaux and Marion Velten et al. reported aptamers with affinity for Unr in their article published in 1999[1].SELEX
In their work published in 1999, Gerard Triqueneaux and Marion Velten et al. used SELEX to isolate RNA aptamer sequences with affinity for Unr from a nucleic acid library containing about 3×1012 unique sequences after 5 rounds of selection process[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the prediction results of the RNA fold website by ribodraw tool to draw[1].5'-CCCGGUGGUUGCUGUAAUUAAGAAAGAACGGAACCAUGGUCAACUAUAUUUAUCACGGGU-3'
Ligand information
SELEX ligand
Unr, also called CSDE1. In molecular biology, the cold-shock domain (CSD) is a protein domain of about 70 amino acids which has been found in prokaryotic and eukaryotic DNA-binding proteins. Part of this domain is highly similar to the RNP-1 RNA-binding motif.-----From Wikipedia
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Unr | O75534 | PF00313 | 88.885 kDa | MSFDPNLLHNNGHNGYPNGTSAALRETGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSSDRRTGKPIAVKLVKIKQEILPEERMNGQVVCAVPHNLESKSPAAPGQSPTGSVCYERNGEVFYLTYTPEDVEGNVQLETGDKINFVIDNNKHTGAVSARNIMLLKKKQARCQGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTIKDRNGKEVATDVRLLPQGTVIFEDISIEHFEGTVTKVIPKVPSKNQNDPLPGRIKVDFVIPKELPFGDKDTKSKVTLLEGDHVRFNISTDRRDKLERATNIEVLSNTFQFTNEAREMGVIAAMRDGFGFIKCVDRDVRMFFHFSEILDGNQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKGTVSFHSHSDHRFLGTVEKEATFSNPKTTSPNKGKEKEAEDGIIAYDDCGVKLTIAFQAKDVEGSTSPQIGDKVEFSISDKQRPGQQVATCVRLLGRNSNSKRLLGYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGNKVSAEKVNKTHSVNGITEEADPTIYSGKVIRPLRSVDPTQTEYQGMIEIVEEGDMKGEVYPFGIVGMANKGDCLQKGESVKFQLCVLGQNAQTMAYNITPLRRATVECVKDQFGFINYEVGDSKKLFFHVKEVQDGIELQAGDEVEFSVILNQRTGKCSACNVWRVCEGPKAVAAPRPDRLVNRLKNITLDDASAPRLMVLRQPRGPDNSMGFGAERKIRQAGVID |
1WFQ 1X65 2YTV |
7812 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| 77 aptamer | 5'-CCCGGUGGUUGCUGUAAUUAAGAAAGAACGGAACCAUGGUCAACUAUAUUUAUCACGGGU-3' | Unr | 10 nM |
| 78 aptamer | 5'-CCCGGUGGUUGCUGUAAUUGAAAAAAAAACAAGAAGAAGGUCAACUAUAUUUAUCACGGGU-3' | Unr | 8 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 |
|---|---|---|---|
| 7ZHH-A | 9.9 | 2.1 | Upstream of N-ras, isoform A |
| 6Y6E-A | 9.8 | 4.8 | Upstream of N-ras, isoform A |
| 2K5N-A | 9.0 | 2.5 | Putative cold-shock protein |
| 3AQQ-A | 8.4 | 1.9 | Calcium-regulated heat stable protein 1 |
| 8EZ6-A | 7.8 | 2.2 | Cell cycle and apoptosis regulator protein 2 |
| 2LSS-A | 7.8 | 2.0 | Cold shock-like protein |
| 2YTX-A | 7.6 | 3.8 | Cold shock domain-containing protein E1 |
| 2KCM-A | 7.6 | 3.1 | Cold shock domain family protein |
| 5UDZ-A | 7.4 | 3.1 | Protein lin-28 homolog A |
| 2MO0-A | 6.8 | 1.7 | Cold-shock DNA-binding domain protein |
References
[1] RNA binding specificity of Unr, a protein with five cold shock domains.Triqueneaux, G., Velten, M., Franzon, P., Dautry, F., & Jacquemin-Sablon, H.
Nucleic acids research, 27(8), 1926–1934. (1999)