Upstream of N-Ras aptamer

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Description

Jacquemin-Sablon, H. et al. reported aptamers with affinity for Unr in their article published in 1999. The 77 aptamer was named by Jacquemin-Sablon, H. et al. in the article[1].



SELEX

In their work published in 1999, Jacquemin-Sablon, H. 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. Before selection, 5 μg of purified His-UNR protein were combined with 25 μl of agarose pre-equilibrated with RNA selection buffer[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 online secondary structure prediction tool to draw. The figure shows the secondary structure prediction of the original aptamer sequence. The main part of this aptamer is a stem loop with a large bulge[1].

5'-CCCGGUGGUUGCUGUAAUUAAGAAAGAACGGAACCAUGGUCAACUAUAUUUAUCACGGGU-3'

drawing


Ligand information

SELEX ligand

Upstream of N-Ras (Unr) protein, 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. Unr is RNA-binding protein involved in translationally coupled mRNA turnover which implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. -----From Uniprot

UniProt ID: uniquely identifies protein sequences in the UniProt database, a resource for protein information.

Pfam: a widely recognised database of protein families and domains.

GenBank: maintained by NCBI(National Center for Biotechnology Information), is a database of nucleotide sequences from various organisms, vital for genetic and molecular biology research.

Mass: an intrinsic property of a body.

Name Uniprot ID Pfam Mass Protein sequence PDB ID GenBank
Unr O75534 PF00313 88.885 kDa
...... MSFDPNLLHNNGHNGYPNGTSAALRETGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSSDRRTGKPIAVKLVKIKQEILPEERMNGQVVCAVPHNLESKSPAAPGQSPTGSVCYERNGEVFYLTYTPEDVEGNVQLETGDKINFVIDNNKHTGAVSARNIMLLKKKQARCQGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTIKDRNGKEVATDVRLLPQGTVIFEDISIEHFEGTVTKVIPKVPSKNQNDPLPGRIKVDFVIPKELPFGDKDTKSKVTLLEGDHVRFNISTDRRDKLERATNIEVLSNTFQFTNEAREMGVIAAMRDGFGFIKCVDRDVRMFFHFSEILDGNQLHIADEVEFTVVPDMLSAQRNHAIRIKKLPKGTVSFHSHSDHRFLGTVEKEATFSNPKTTSPNKGKEKEAEDGIIAYDDCGVKLTIAFQAKDVEGSTSPQIGDKVEFSISDKQRPGQQVATCVRLLGRNSNSKRLLGYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGNKVSAEKVNKTHSVNGITEEADPTIYSGKVIRPLRSVDPTQTEYQGMIEIVEEGDMKGEVYPFGIVGMANKGDCLQKGESVKFQLCVLGQNAQTMAYNITPLRRATVECVKDQFGFINYEVGDSKKLFFHVKEVQDGIELQAGDEVEFSVILNQRTGKCSACNVWRVCEGPKAVAAPRPDRLVNRLKNITLDDASAPRLMVLRQPRGPDNSMGFGAERKIRQAGVID
1WFQ
1X65
2YTV 		7812

Some isolated sequences bind to the affinity of the protein[1].

Name Sequence Ligand Affinity
77 aptamer 5'-CCCGGUGGUUGCUGUAAUUAAGAAAGAACGGAACCAUGGUCAACUAUAUUUAUCACGGGU-3' Unr 10 nM
78 aptamer 5'-CCCGGUGGUUGCUGUAAUUGAAAAAAAAACAAGAAGAAGGUCAACUAUAUUUAUCACGGGU-3' Unr 8 nM
drawing

Similar compound(s)

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.

Dail server website: a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB).

Z-score: 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) is used to measure the degree to which atoms deviate from the alignment position.

PDB: PDB ID+ chain name.

PDB Z-socre RMSD (Å) Description
1WFQ-A 18.8 0 Original chain
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)