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21.01 aptamer
Description
Michiko Kimoto and Kensaku Sakamoto et al. reported aptamers with affinity for Raf-1 in their article published in 1998[1].SELEX
In their work published in 1998, Michiko Kimoto and Kensaku Sakamoto et al. used SELEX to isolate RNA aptamer sequences with affinity for Raf-1 from a nucleic acid library containing about 8×1013 108-nucleotide sequences with after 13 rounds of selection process[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'-CUGAUCAAUGGCGUACAAUGGAUUCGUUCUCAUAACCAAAACCCUUACCCCUUGGACUGA-3'
Ligand information
SELEX ligand
RAF proto-oncogene serine/threonine-protein kinase that acts as a regulatory link between the membrane-associated Ras GTPases and the MAPK/ERK cascade, and this critical regulatory link functions as a switch determining cell fate decisions including proliferation, differentiation, apoptosis, survival and oncogenic transformation. RAF1 activation initiates a mitogen-activated protein kinase cascade that comprises a sequential phosphorylation of the dual-specific MAPK kinases and the extracellular signal-regulated kinases. The phosphorylated form of RAF1 phosphorylates BAD/Bcl2-antagonist of cell death at 'Ser-75'. Phosphorylates adenylyl cyclases: ADCY2, ADCY5 and ADCY6, resulting in their activation.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Raf-1 | P04049 | PF00069 | 73.052 kDa | MEHIQGAWKTISNGFGFKDAVFDGSSCISPTIVQQFGYQRRASDDGKLTDPSKTSNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTDAASLIGEELQVDFLDHVPLTTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMCVDWSNIRQLLLFPNSTIGDSGVPALPSLTMRRMRESVSRMPVSSQHRYSTPHAFTFNTSSPSSEGSLSQRQRSTSTPNVHMVSTTLPVDSRMIEDAIRSHSESASPSALSSSPNNLSPTGWSQPKTPVPAQRERAPVSGTQEKNKIRPRGQRDSSYYWEIEASEVMLSTRIGSGSFGTVYKGKWHGDVAVKILKVVDPTPEQFQAFRNEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLIDIARQTAQGMDYLHAKNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQVEQPTGSVLWMAPEVIRMQDNNPFSFQSDVYSYGIVLYELMTGELPYSHINNRDQIIFMVGRGYASPDLSKLYKNCPKAMKRLVADCVKKVKEERPLFPQILSSIELLQHSLPKINRSASEPSLHRAAHTEDINACTLTTSPRLPVF | 1GUA | 5894 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| 21.01 aptamer | 5'-CUGAUCAAUGGCGUACAAUGGAUUCGUUCUCAUAACCAAAACCCUUACCCCUUGGACUGA-3' | Raf-1 | 332 ± 93 nM |
| 21.07 aptamer | 5'-UUGACUCAAUGGCGUACAAUGGAUUCGUUCUCAUAACCAAAACCCUUACCCCUUGGACUG-3' | Raf-1 | 332 ± 93 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 |
|---|---|---|---|
| 6GOM-D | 28.0 | 1.0 | GTPase kRas |
| 2WKP-A | 25.1 | 1.6 | NPH1-1, Ras-related C3 botulinum toxin substrate |
| 6JMG-A | 24.4 | 1.8 | DNAj homolog subfamily C member 27-A |
| 5C2K-A | 22.9 | 1.7 | Transforming protein Rhoa, Rac GTPase-activating P |
| 2IWR-A | 22.3 | 1.9 | Centaurin gamma 1 |
| 5JCP-A | 22.1 | 1.8 | Arf-gap with Rho-Gap domain, ank repeat and PH DO |
| 6BBP-A | 19.6 | 2.1 | Cytohesin-3, ADP-ribosylation factor 6 |
| 3LVQ-E | 19.5 | 2.2 | Arf-gap with SH3 domain, ank repeat and PH domain |
| 2MMC-A | 17.9 | 1.9 | GTP-binding nuclear protein Ran |
| 6VIH-B | 17.9 | 2.2 | Rab-like protein 3 |
References
[1] RNA aptamers that specifically bind to the Ras-binding domain of Raf-1.Kimoto, M., Sakamoto, K., Shirouzu, M., Hirao, I., & Yokoyama, S.
FEBS letters, 441(2), 322–326. (1998)