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Hemagglutinin (HA) protein-aptamer
Description
In 2014, Hyun-Mi Kwon and colleagues used SELEX (Systematic Evolution of Ligands by Exponential enrichment) technique to isolate high affinity RNA aptamers that bind to the HA protein[1].SELEX
In 2014, Hyun-Mi Kwon, Kwang Hyun Lee , et al. isolated 1 specific sequences targeting Hemagglutinin (HA) proteinafter 12 rounds of selection[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'-GCUUGACGGAGAUCAAGGGCGAGUCUCAUACCAAGUUGAUGGGG-3'
Ligand information
SELEX ligand
The haemagglutinin(British English) is a homotrimeric glycoprotein found on the surface of influenza viruses and is integral to its infectivity. encapsidation and repression of replicase translation-by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication.-----from Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Hemagglutinin (HA) | P03436 | PF00509 | 63.488 kDa | MKTIIALSYIFCLALGQDLPGNDNNTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPDSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGQSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTRGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVVLLGFIMWACQRGNIRCNICI | 5T6N | 3654620 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| HA12-16 | 5'-GCUUGACGGAGAUCAAGGGCGAGUCGCAUACCAAGUUGAUGGGG-3' | Haemagglutinin | 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 |
|---|---|---|---|
| 5UMN-B | 36.7 | 0.8 | Hemagglutinin |
| 4F23-A | 27.9 | 2.5 | Hemagglutinin |
| 6CNV-A | 22.0 | 3.9 | Hemagglutinin |
| 1FLC-A | 12.5 | 5.0 | Haemagglutinin-esterase-fusion glycoprotein |
| 5JIF-A | 11.3 | 4.0 | Hemagglutinin-esterase |
| 7JS4-A | 5.3 | 31.6 | F5/8 type c domain protein |
| 5CJQ-A | 4.9 | 1.7 | Cr9114 light chain |
| 4W8J-A | 4.5 | 21.1 | Pesticidal crystal protein cry1ac |
| 8A28-A | 4.4 | 4.4 | Metalloendopeptidase |
| 6Y5L-A | 4.3 | 1.5 | Influenza |
References
[1] An RNA aptamer that specifically binds to the glycosylated hemagglutinin of avian influenza virus and suppresses viral infection in cells.Kwon, H. M., Lee, K. H., Han, B. W., Han, M. R., Kim, D. H., & Kim, D. E.
PloS one, 9(5), e97574. (2014)