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ZAP-aptamer
Description
In 2010, Huang et al. used the SELEX method to isolate ZAP-binding RNAaptamers. After 21 rounds of selection, ZAP-binding aptamers were isolated. Sequence analysis revealed that they are G-rich RNAs with predicted stem-loop structures containing conserved “GGGUGG” and “GAGGG” motifs in the loop region[1].SELEX
In 2010, Huang et al. used the SELEX method to isolate the aptamer with 40 nucleotides of random sequence, after 21 rounds of selection. Sequence analysis revealed that they are G-rich RNAs with predicted stem-loop structures containing conserved “GGGUGG” and “GAGGG” motifs in the loop region[1].
Detailed information are accessible on SELEX page.
Structure
21E was the aptamer sequence mainly studied in the article, which had a high affinity with ZAP. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-GGGAACAGUCCGAGCCUGCGUGCGAGGAGGUGGAGAGGGUGGGUGUGCGUGGCGUGGGGUGAAUUCGUCAUA-3'
Ligand information
SELEX ligand
Zinc-finger antiviral protein (ZAP) is a host factor that specifically inhibits the replication of certain viruses, such as HIV-1, by targeting viral mRNA for degradation. N-terminal domain of ZAP is the major functional domain which contains four zinc-finger motifs. This entry represents the third zinc finger type CCCH.-----from Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Zinc-finger antiviral protein (ZAP) | Q8K3Y6 | IPR040954 | 26.21 kDa | GPLGMADPGVCCFITKILCAHGGRMTLEELLGEIRLPEAQLYELLETAGPDRFVLLETGGQAGITRSVVATTRARVCRRKYCQRPCDSLHLCKLNLLGRCHYAQSQRNLCKYSHDVLSEQNFQILKNHELSGLNQEELACLLVQSDPFFLPEICKSYKGEGRKQTCGQPQPCERLHICEHFTRGNCSYLNCLRSHNLMDRKVLTIMREHGLSPDVVQNIQDICNNKHAR | 3U9G | ADD71159.1 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| 21E | 5'-UGCGUGCGAGGAGGUGGAGAGGGUGGGUGUGCGUGGCGUG-3' | Zinc-finger antiviral protein (ZAP) | NA |
| 21K | 5'-GGGAACAGUCCGAGCCAAGCGGUAGCGUCAGGGGGUGGAGGGAGGAGGCCGCGUGGUGUGGGUGAAUUCGUCAUA-3' | Zinc-finger antiviral protein (ZAP) | NA |
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 |
|---|---|---|---|
| 3U9G-A | 37.2 | 0.0 | Zinc finger CCCH-type antiviral Protein 1 |
| 2ZKZ-C | 5.5 | 2.2 | Transcriptional repressor pagr |
| 2RDP-A | 5.5 | 2.7 | Putative transcriptional regulator marr |
| 7EL3-A | 5.4 | 2.8 | Homoprotocatechuate degradation operon regulator |
| 7WZE-A | 5.3 | 3.1 | Uncharacterized HTH-type transcriptional regulato |
| 3S2W-A | 5.2 | 2.9 | Transcriptional regulator, marr family |
| 2WTE-A | 5.2 | 2.8 | CSA3 |
| 3BPX-A | 5.0 | 3.0 | Transcriptional regulator, marr family |
| 3VB2-B | 5.0 | 2.5 | Multiple antibiotic resistance protein marr |
| 2NYX-B | 4.9 | 2.9 | Probable transcriptional regulatory protein, RV14 |
References
[1] Analyses of SELEX-derived ZAP-binding RNA aptamers suggest that the binding specificity is determined by both structure and sequence of the RNA.Huang, Z., Wang, X., & Gao, G.
Protein Cell, 1(8), 752-9. (2010)