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TbRIII-aptamer
Description
In 2006, Ohuchi, S. P., Ohtsu, T., & Nakamura, Y. developed a novel SELEX procedure (referred to as TECS-SELEX) in which cell-surface displayed recombinant protein is directly used as the selection target. Using this method, they isolated RNA aptamers against transforming growth factor-beta type III receptor expressed on Chinese hamster ovary (CHO) cells. One of the RNA aptamers has a dissociation constant in the 1 nM range and competed with transforming growth factor-beta to bind to the cell surface receptor in vitro[1].SELEX
In 2006, Ohuchi, S. P., Ohtsu, T., & Nakamura, Y. carried out SELEX using Chinese hamster ovary (CHO) cells ectopically expressing human transforming growth factor-β (TGF-β) type III receptor (TbRIII) on the cell surface. After 11 rounds of the TECS-SELEX, an RNA aptamer against TbRIII with high affinity and specificity to its functional form on the cell surface was isolated[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'-GGGCCAGGCAGCGAGAGATAAGCAGAAGAAGTATGTGACCATGCTCCAGAGAGCAACTTCACATGCGTAGCCAAACCGACCACACGCGTCCGAGA-3'
Ligand information
SELEX ligand
Binds to TGF-beta. Could be involved in capturing and retaining TGF-beta for presentation to the signaling receptors (By similarity). In gonadotrope cells, acts as an inhibin A coreceptor and regulates follicle-stimulating hormone (FSH) levels and female fertility.-----from uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| TbRIII | O88393 | PF00680 | 19.00 kDa | TFNMELYNTDLFLVPSPGVFSVAENEHVYVEVSVTKADQDLGFAIQTCFISPYSNPDRMSDYTIIENICPKDDSVKFYSSKRVHFPIPHAEVDKKRFSFVFKSVFNTSLLFLHCELTLCSRNKGSQKLPKCVTPDDACTSLDATMIWTMMQNKKTFTKPLAVVLQVD | 4AJV | 21814 |
Some isolated sequences bind to the affinity of the protein..
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| A07 aptamer | 5'-GGGCCAGGCAGCGAGAGATAAGCAGAAGAAGTATGTGACCATGCTCCAGAGAGCAACTTCACATGCGTAGCCAAACCGACCACACGCGTCCGAGA-3' | TbRIII | 2.47 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 |
|---|---|---|---|
| 3QW9-A | 23.9 | 1.4 | Transforming growth |
| 5BUP-A | 14.3 | 2.6 | Zona pellucida sperm-binding protein 2 |
| 4WRN-A | 13.6 | 2.2 | Maltose-binding periplasmic protein,uromodulin |
| 5HZV-A | 12.8 | 2.3 | Maltose-binding periplasmic protein,endoglin |
| 7PFP-A | 11.7 | 4.0 | Uromodulin |
| 8BQU-A | 11.3 | 2.5 | Zona pellucida sperm-binding protein 3 |
| 8RKI-B | 11.1 | 2.4 | Zona pellucida sperm-binding protein 3 |
| 4OF3-B | 9.3 | 3.3 | Protein syg-1, isoform b |
| 5T89-Y | 7.4 | 2.7 | Vascular endothelial growth factor a |
| 2DAV-A | 7.3 | 2.6 | Myosin-binding protein c, slow-type |
References
[1] Selection of RNA aptamers against recombinant transforming growth factor-beta type III receptor displayed on cell surface.Ohuchi, S. P., Ohtsu, T., & Nakamura, Y.
Biochimie, 88(7), 897–904. (2006)