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E2F-E1 aptamer
Description
Jun Ishizaki and Joseph R. Nevins et al. reported aptamers with affinity for E2F1 in their article published in 1996[1].SELEX
In their work published in 1996, Jun Ishizaki and Joseph R. Nevins et al. used SELEX to isolate RNA aptamer sequences with affinity for E2F1 from a nucleic acid library containing about 1015 sequences[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-AGAGCGGAAGCGUGCUGGGCCAUGGAGUCGAUGUGAUAAGUAGGACGGAGGUGGUCGAUAGGGGGGAUCCAUCGACCUCUGGGUUAUG-3'
Ligand information
SELEX ligand
E2F is transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from g1 to s phase. E2F2 binds specifically to RB1 in a cell-cycle dependent manner.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| E2F | Q14209 | PF02319 | 47.506 kDa | MLQGPRALASAAGQTPKVVPAMSPTELWPSGLSSPQLCPATATYYTPLYPQTAPPAAAPGTCLDATPHGPEGQVVRCLPAGRLPAKRKLDLEGIGRPVVPEFPTPKGKCIRVDGLPSPKTPKSPGEKTRYDTSLGLLTKKFIYLLSESEDGVLDLNWAAEVLDVQKRRIYDITNVLEGIQLIRKKAKNNIQWVGRGMFEDPTRPGKQQQLGQELKELMNTEQALDQLIQSCSLSFKHLTEDKANKRLAYVTYQDIRAVGNFKEQTVIAVKAPPQTRLEVPDRTEDNLQIYLKSTQGPIEVYLCPEEVQEPDSPSEEPLPSTSTLCPSPDSAQPSSSTDPSIMEPTASSVPAPAPTPQQAPPPPSLVPLEATDSLLELPHPLLQQTEDQFLSPTLACSSPLISFSPSLDQDDYLWGLEAGEGISDLFDSYDLGDLLIN | 1N4M | 1870 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| E2F-E1 aptamer | 5'-AGAGCGGAAGCGUGCUGGGCCAUGGAGUCGAUGUGAUAAGUAGGACGGAGGUGGUCGAUAGGGGGGAUCCAUCGACCUCUGGGUUAUG-3' | E2F protein | 4 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 |
|---|---|---|---|
| 4ELJ-A | 31.1 | 1.7 | Retinoblastoma-associated protein |
| 2W2H-A | 9.9 | 3.2 | Cyclin-T1 |
| 7JV7-B | 9.8 | 3.5 | CTD kinase subunit alpha |
| 7XQK-B | 9.8 | 2.8 | Glutathione S-transferase class-Mu 26 kDa isozyme |
| 6CNB-R | 9.7 | 13.2 | DNA-directed RNA polymerase III subunit RPC1 |
| 7ZS9-M | 9.5 | 19.2 | DNA-directed RNA polymerase II subunit RPB1 |
| 7KPV-B | 9.5 | 3.7 | Meiotic mRNA stability protein kinase SSN3 |
| 7NJ0-C | 9.4 | 3.3 | Securin,separin |
| 2W96-A | 9.1 | 2.9 | Cell division protein kinase 4 |
| 5IY7-M | 9.0 | 8.8 | DNA-directed RNA polymerase II subunit RPB1 |
References
[1] Inhibition of cell proliferation by an RNA ligand that selectively blocks E2F function.Ishizaki, J., Nevins, J. R., & Sullenger, B. A.
Nature medicine, 2(12), 1386–1389. (1996)