E2F1 aptamer

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Description

Sullenger, B. A. et al. reported aptamers with affinity for E2F1 in their article published in 1996. The E2F-E1 aptamer was named by Sullenger, B. A. et al. in the article[1].



SELEX

In their work published in 1996, Sullenger, B. A. Nevins et al. used SELEX to isolate RNA aptamer sequences with affinity for E2F1 from a nucleic acid library containing about 1015 sequences. Protein-RNA complexes were filtered through a wet nitrocellulose filter in a pop-top filter holder then washed using binding buffer[1].

Detailed information are accessible on SELEX page.



Structure

The 2D structure of the figure is based on the article by online secondary structure prediction tool to draw. The figure shows the secondary structure prediction of the original aptamer sequence. This aptamer contains three stem loops of varying lengths. The longest stem loop has three bulge and is the main part of the aptamer[1].

5'-AGAGCGGAAGCGUGCUGGGCCAUGGAGUCGAUGUGAUAAGUAGGACGGAGGUGGUCGAUAGGGGGGAUCCAUCGACCUCUGGGUUAUG-3'

drawing


Ligand information

SELEX ligand

E2F is transcription activator that binds DNA cooperatively with docking 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

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
E2F Q14209 PF02319 47.506 kDa
...... MLQGPRALASAAGQTPKVVPAMSPTELWPSGLSSPQLCPATATYYTPLYPQTAPPAAAPGTCLDATPHGPEGQVVRCLPAGRLPAKRKLDLEGIGRPVVPEFPTPKGKCIRVDGLPSPKTPKSPGEKTRYDTSLGLLTKKFIYLLSESEDGVLDLNWAAEVLDVQKRRIYDITNVLEGIQLIRKKAKNNIQWVGRGMFEDPTRPGKQQQLGQELKELMNTEQALDQLIQSCSLSFKHLTEDKANKRLAYVTYQDIRAVGNFKEQTVIAVKAPPQTRLEVPDRTEDNLQIYLKSTQGPIEVYLCPEEVQEPDSPSEEPLPSTSTLCPSPDSAQPSSSTDPSIMEPTASSVPAPAPTPQQAPPPPSLVPLEATDSLLELPHPLLQQTEDQFLSPTLACSSPLISFSPSLDQDDYLWGLEAGEGISDLFDSYDLGDLLIN
1N4M 1870

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

Name Sequence Ligand Affinity
E2F-E1 aptamer 5'-AGAGCGGAAGCGUGCUGGGCCAUGGAGUCGAUGUGAUAAGUAGGACGGAGGUGGUCGAUAGGGGGGAUCCAUCGACCUCUGGGUUAUG-3' E2F protein 4 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
1N4M-A 54.4 0 Original chain
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)