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TR-D28 aptamer
Description
Michael Blind and Waldemar Kolanus et al. reported aptamers with affinity for CD18 in their article published in 1998[1].SELEX
In their work published in 1999, Michael Blind and Waldemar Kolanus et al. used SELEX to isolate RNA aptamer sequences with affinity for CD18 from a nucleic acid library containing about 5×1014 sequences with after 11 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'-GGGCGCUAAGUCCUCGCUCAUACAACGAGGGGUCGUGUAGGGAUGUAUGGGCUUGGACACACGCGCGACUCGGAUCCUAC-3'
Ligand information
SELEX ligand
In molecular biology, CD18 (Integrin beta chain-2) is an integrin beta chain protein that is encoded by the ITGB2 gene in humans. Upon binding with one of a number of alpha chains, CD18 is capable of forming multiple heterodimers, which play significant roles in cellular adhesion and cell surface signaling, as well as important roles in immune responses. CD18 also exists in soluble, ligand binding forms. Deficiencies in CD18 expression can lead to adhesion defects in circulating white blood cells in humans, reducing the immune system's ability to fight off foreign invaders.-----From Wikipedia
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| CD18 | CD18 | PF00362 | 84.791 kDa | MLGLRPPLLALVGLLSLGCVLSQECTKFKVSSCRECIESGPGCTWCQKLNFTGPGDPDSIRCDTRPQLLMRGCAADDIMDPTSLAETQEDHNGGQKQLSPQKVTLYLRPGQAAAFNVTFRRAKGYPIDLYYLMDLSYSMLDDLRNVKKLGGDLLRALNEITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPFAFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEIGWRNVTRLLVFATDDGFHFAGDGKLGAILTPNDGRCHLEDNLYKRSNEFDYPSVGQLAHKLAENNIQPIFAVTSRMVKTYEKLTEIIPKSAVGELSEDSSNVVHLIKNAYNKLSSRVFLDHNALPDTLKVTYDSFCSNGVTHRNQPRGDCDGVQINVPITFQVKVTATECIQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSSQELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQCERTTEGCLNPRRVECSGRGRCRCNVCECHSGYQLPLCQECPGCPSPCGKYISCAECLKFEKGPFGKNCSAACPGLQLSNNPVKGRTCKERDSEGCWVAYTLEQQDGMDRYLIYVDESRECVAGPNIAAIVGGTVAGIVLIGILLLVIWKALIHLSDLREYRRFEKEKLKSQWNNDNPLFKSATTTVMNPKFAES |
1YUK 2P26 3K6S |
3689 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| TR-D28 aptamer | 5'-GGGCGCUAAGUCCUCGCUCAUACAACGAGGGGUCGUGUAGGGAUGUAUGGGCUUGGACACACGCGCGACUCGGAUCCUAC-3' | CD18 | 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 |
|---|---|---|---|
| 5E6W-A | 24.0 | 6.1 | Integrin beta-2 |
| 1JV2-B | 15.0 | 2.3 | Integrin, alpha V |
| 8T2V-B | 14.2 | 4.7 | Integrin alpha-IIB |
| 8JMW-A | 9.5 | 11.3 | S8 family serine peptidase |
| 6FVI-A | 9.0 | 2.1 | Centrosomal protein of 192 kDa |
| 8K2G-A | 8.4 | 3.1 | Oligosaccharide-releasing beta-N-acetylgalactosam |
| 7PTB-A | 8.3 | 8.5 | Centrosomal protein of 192 kDa |
| 2E6J-A | 8.3 | 2.1 | Hydin protein |
| 6LP4-A | 8.3 | 2.5 | Vesicle-associated membrane protein-associated PR |
| 4UJ6-A | 8.1 | 12.4 | Surface layer protein |
References
[1] Cytoplasmic RNA modulators of an inside-out signal-transduction cascade.Blind, M., Kolanus, W., & Famulok, M.
Proceedings of the National Academy of Sciences of the United States of America, 96(7), 3606–3610. (1999)