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SE RNA #1 aptamer
Description
Soo-Jin Bae and Ji-Hyun Oum et al. reported aptamers with affinity for nuclear factor of activated T cells in their article published in 2002[1].SELEX
In their work published in 2002, Soo-Jin Bae and Ji-Hyun Oum et al. used SELEX to isolate RNA aptamer sequences with affinity for nuclear factor of activated T cells from a nucleic acid library containing about 1014 94-nucleotides-long sequences after 10 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'-GGGAGAGCGGAAGCGUGCUGGGCCUCUGUUCCCAAGGGAAUACUGGUCGUGUUGGAUCAGGUUGGCAUAACCCAGAGGUCGAUGGAUCCCCCC-3'
Ligand information
SELEX ligand
NFATC1 plays a role in the inducible expression of cytokine genes in T-cells, especially in the induction of the IL-2 or IL-4 gene transcription. Also controls gene expression in embryonic cardiac cells. Could regulate not only the activation and proliferation but also the differentiation and programmed death of T-lymphocytes as well as lymphoid and non-lymphoid cells.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| NFATC1 | O95644 | PF00554 | 101.243 kDa | MPSTSFPVPSKFPLGPAAAVFGRGETLGPAPRAGGTMKSAEEEHYGYASSNVSPALPLPTAHSTLPAPCHNLQTSTPGIIPPADHPSGYGAALDGGPAGYFLSSGHTRPDGAPALESPRIEITSCLGLYHNNNQFFHDVEVEDVLPSSKRSPSTATLSLPSLEAYRDPSCLSPASSLSSRSCNSEASSYESNYSYPYASPQTSPWQSPCVSPKTTDPEEGFPRGLGACTLLGSPRHSPSTSPRASVTEESWLGARSSRPASPCNKRKYSLNGRQPPYSPHHSPTPSPHGSPRVSVTDDSWLGNTTQYTSSAIVAAINALTTDSSLDLGDGVPVKSRKTTLEQPPSVALKVEPVGEDLGSPPPPADFAPEDYSSFQHIRKGGFCDQYLAVPQHPYQWAKPKPLSPTSYMSPTLPALDWQLPSHSGPYELRIEVQPKSHHRAHYETEGSRGAVKASAGGHPIVQLHGYLENEPLMLQLFIGTADDRLLRPHAFYQVHRITGKTVSTTSHEAILSNTKVLEIPLLPENSMRAVIDCAGILKLRNSDIELRKGETDIGRKNTRVRLVFRVHVPQPSGRTLSLQVASNPIECSQRSAQELPLVEKQSTDSYPVVGGKKMVLSGHNFLQDSKVIFVEKAPDGHHVWEMEAKTDRDLCKPNSLVVEIPPFRNQRITSPVHVSFYVCNGKRKRSQYQRFTYLPANVPIIKTEPTDDYEPAPTCGPVSQGLSPLPRPYYSQQLAMPPDPSSCLVAGFPPCPQRSTLMPAAPGVSPKLHDLSPAAYTKGVASPGHCHLGLPQPAGEAPAVQDVPRPVATHPGSPGQPPPALLPQQVSAPPSSSCPPGLEHSLCPSSPSPPLPPATQEPTCLQPCSPACPPATGRPQHLPSTVRRDESPTAGPRLLPEVHEDGSPNLAPIPVTVKREPEELDQLYLDDVNEIIRNDLSSTSTHS | 5SVE | 4772 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| SE RNA #1 aptamer | 5'-GGGAGAGCGGAAGCGUGCUGGGCCUCUGUUCCCAAGGGAAUACUGGUCGUGUUGGAUCAGGUUGGCAUAACCCAGAGGUCGAUGGAUCCCCCC-3' | NFATC | 30 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 |
|---|---|---|---|
| 4IL1-A | 55.9 | 1.0 | Calmodulin, calcineurin subunit B type 1, serine/ |
| 1WAO-1 | 43.7 | 4.8 | Serine/threonine protein phosphatase 5 |
| 6ZEJ-I | 42.3 | 1.8 | Serine/threonine-protein phosphatase PP1-Alpha CA |
| 2Z72-A | 20.8 | 3.4 | Protein-tyrosine-phosphatase |
| 2DFJ-A | 17.2 | 2.8 | Diadenosinetetraphosphatase |
| 1G5B-B | 16.7 | 2.8 | Serine/threonine protein phosphatase |
| 2QJC-A | 16.5 | 2.9 | Diadenosine tetraphosphatase, putative |
| 2GJU-A | 15.5 | 3.1 | 252aa long hypothetical protein |
| 5VJV-A | 15.0 | 3.0 | Rhizobiales-like phosphatase 2 |
| 3QFM-A | 13.6 | 3.1 | Putative uncharacterized protein |
References
[1] In vitro selection of specific RNA inhibitors of NFATc.Bae, S. J., Oum, J. H., Sharma, S., Park, J., & Lee, S. W.
Biochemical and biophysical research communications, 298(4), 486–492. (2002)