Activated T Cells' Nuclear Factor aptamer

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Description

Lee, S. W. et al. reported aptamers with affinity for nuclear factor of activated T cells in their article published in 2002. The SE RNA #1 aptamer was named by Lee, S. W. et al. in the article[1].



SELEX

In their work published in 2002, Lee, S. W. 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. To remove nonspecific RNAs with binding activity to agarose beads, the RNA library was pre-incubated with agarose beads[1].

Detailed information are accessible on SELEX page.



Structure

The 2D structure of the figure is based on the article by online secondary structure prediction tool to draw. The figure shows the secondary structure prediction of the original aptamer sequence. This aptamer contains three stem loops of different lengths with G-U non-canonical base pairings. Three stem loops are connected by two junctions. The 5' and 3' ends of aptamer each has an overhang[1].

5'-GGGAGAGCGGAAGCGUGCUGGGCCUCUGUUCCCAAGGGAAUACUGGUCGUGUUGGAUCAGGUUGGCAUAACCCAGAGGUCGAUGGAUCCCCCC-3'

drawing


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. NFATC1 also controls gene expression in embryonic cardiac cells. It 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. It is also required for osteoclastogenesis and regulates many genes important for osteoclast differentiation and function.-----From Uniprot

UniProt ID: uniquely identifies protein sequences in the UniProt database, a resource for protein information.

Pfam: a widely recognised database of protein families and domains.

GenBank: maintained by NCBI(National Center for Biotechnology Information), is a database of nucleotide sequences from various organisms, vital for genetic and molecular biology research.

Mass: an intrinsic property of a body.

Name Uniprot ID Pfam Mass Protein sequence PDB ID GenBank
NFATC1 O95644 PF00554 101.243 kDa
...... MPSTSFPVPSKFPLGPAAAVFGRGETLGPAPRAGGTMKSAEEEHYGYASSNVSPALPLPTAHSTLPAPCHNLQTSTPGIIPPADHPSGYGAALDGGPAGYFLSSGHTRPDGAPALESPRIEITSCLGLYHNNNQFFHDVEVEDVLPSSKRSPSTATLSLPSLEAYRDPSCLSPASSLSSRSCNSEASSYESNYSYPYASPQTSPWQSPCVSPKTTDPEEGFPRGLGACTLLGSPRHSPSTSPRASVTEESWLGARSSRPASPCNKRKYSLNGRQPPYSPHHSPTPSPHGSPRVSVTDDSWLGNTTQYTSSAIVAAINALTTDSSLDLGDGVPVKSRKTTLEQPPSVALKVEPVGEDLGSPPPPADFAPEDYSSFQHIRKGGFCDQYLAVPQHPYQWAKPKPLSPTSYMSPTLPALDWQLPSHSGPYELRIEVQPKSHHRAHYETEGSRGAVKASAGGHPIVQLHGYLENEPLMLQLFIGTADDRLLRPHAFYQVHRITGKTVSTTSHEAILSNTKVLEIPLLPENSMRAVIDCAGILKLRNSDIELRKGETDIGRKNTRVRLVFRVHVPQPSGRTLSLQVASNPIECSQRSAQELPLVEKQSTDSYPVVGGKKMVLSGHNFLQDSKVIFVEKAPDGHHVWEMEAKTDRDLCKPNSLVVEIPPFRNQRITSPVHVSFYVCNGKRKRSQYQRFTYLPANVPIIKTEPTDDYEPAPTCGPVSQGLSPLPRPYYSQQLAMPPDPSSCLVAGFPPCPQRSTLMPAAPGVSPKLHDLSPAAYTKGVASPGHCHLGLPQPAGEAPAVQDVPRPVATHPGSPGQPPPALLPQQVSAPPSSSCPPGLEHSLCPSSPSPPLPPATQEPTCLQPCSPACPPATGRPQHLPSTVRRDESPTAGPRLLPEVHEDGSPNLAPIPVTVKREPEELDQLYLDDVNEIIRNDLSSTSTHS
5SVE 4772

Some isolated sequences bind to the affinity of the protein[1].

Name Sequence Ligand Affinity
SE RNA #1 aptamer 5'-GGGAGAGCGGAAGCGUGCUGGGCCUCUGUUCCCAAGGGAAUACUGGUCGUGUUGGAUCAGGUUGGCAUAACCCAGAGGUCGAUGGAUCCCCCC-3' NFATC 30 nM
drawing

Similar compound(s)

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.

Dail server website: a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB).

Z-score: 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) is used to measure the degree to which atoms deviate from the alignment position.

PDB: PDB ID+ chain name.

PDB Z-socre RMSD (Å) Description
5SVE-A 61.9 0 Original chain
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)