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W2 aptamer
Description
June Hyung Lee and Hana Kim et al. reported aptamers with affinity for complement component 5 in their article published in 2002[1].SELEX
In their work published in 2002, June Hyung Lee and Hana Kim et al. used SELEX to isolate RNA aptamer sequences with affinity for complement component 5 from a nucleic acid library containing about 5×1014 30-nucleotides-long sequences after 15 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'-CGUCCCUUCGCAACCCUUUAAGACUUGGGACCCUGCUCUU-3'
Ligand information
SELEX ligand
Activation of C5 by a C5 convertase initiates the spontaneous assembly of the late complement components, C5-C9, into the membrane attack complex. C5b has a transient binding site for C6. The C5b-C6 complex is the foundation upon which the lytic complex is assembled.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| C5 protein | P01031 | PF07678 | 188.305 kDa | MGLLGILCFLIFLGKTWGQEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATISIKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSKHFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLTFIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYFEVKEYVLPHFSVSIEPEYNFIGYKNFKNFEITIKARYFYNKVVTEADVYITFGIREDLKDDQKEMMQTAMQNTMLINGIAQVTFDSETAVKELSYYSLEDLNNKYLYIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATPLFLKPGIPYPIKVQVKDSLDQLVGGVPVTLNAQTIDVNQETSDLDPSKSVTRVDDGVASFVLNLPSGVTVLEFNVKTDAPDLPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGEHLNIIVTPKSPYIDKITHYNYLILSKGKIIHFGTREKFSDASYQSINIPVTQNMVPSSRLLVYYIVTGEQTAELVSDSVWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVALAAVDSAVYGVQRGAKKPLERVFQFLEKSDLGCGAGGGLNNANVFHLAGLTFLTNANADDSQENDEPCKEILRPRRTLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVASQLRANISHKDMQLGRLHMKTLLPVSKPEIRSYFPESWLWEVHLVPRRKQLQFALPDSLTTWEIQGVGISNTGICVADTVKAKVFKDVFLEMNIPYSVVRGEQIQLKGTVYNYRTSGMQFCVKMSAVEGICTSESPVIDHQGTKSSKCVRQKVEGSSSHLVTFTVLPLEIGLHNINFSLETWFGKEILVKTLRVVPEGVKRESYSGVTLDPRGIYGTISRRKEFPYRIPLDLVPKTEIKRILSVKGLLVGEILSAVLSQEGINILTHLPKGSAEAELMSVVPVFYVFHYLETGNHWNIFHSDPLIEKQKLKKKLKEGMLSIMSYRNADYSYSVWKGGSASTWLTAFALRVLGQVNKYVEQNQNSICNSLLWLVENYQLDNGSFKENSQYQPIKLQGTLPVEARENSLYLTAFTVIGIRKAFDICPLVKIDTALIKADNFLLENTLPAQSTFTLAISAYALSLGDKTHPQFRSIVSALKREALVKGNPPIYRFWKDNLQHKDSSVPNTGTARMVETTAYALLTSLNLKDINYVNPVIKWLSEEQRYGGGFYSTQDTINAIEGLTEYSLLVKQLRLSMDIDVSYKHKGALHNYKMTDKNFLGRPVEVLLNDDLIVSTGFGSGLATVHVTTVVHKTSTSEEVCSFYLKIDTQDIEASHYRGYGNSDYKRIVACASYKPSREESSSGSSHAVMDISLPTGISANEEDLKALVEGVDQLFTDYQIKDGHVILQLNSIPSSDFLCVRFRIFELFEVGFLSPATFTVYEYHRPDKQCTMFYSTSNIKIQKVCEGAACKCVEADCGQMQEELDLTISAETRKQTACKPEIAYAYKVSITSITVENVFVKYKATLLDIYKTGEAVAEKDSEITFIKKVTCTNAELVKGRQYLIMGKEALQIKYNFSFRYIYPLDSLTWIEYWPRDTTCSSCQAFLANLDEFAEDIFLNGC | 3CU7 | 727 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| W2 aptamer | 5'-CGUCCCUUCGCAACCCUUUAAGACUUGGGACCCUGCUCUU-3' | C5 protein | 3.6 nM |
| W12 aptamer | 5'-GUGCAGGUUUUGAAGAUGUGCCGACUUCUACACCAAACGGCA-3' | C5 protein | 3.8 nM |
| W50 aptamer | 5'-GACUUGUGCAAGAACCCAGUCAAAAGCCGGGCCGUUAAGCUA-3' | C5 protein | 4.3 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 |
|---|---|---|---|
| 5I5K-B | 40.5 | 2.7 | Complement C5 |
| 8OQ3-D | 35.1 | 5.1 | Complement C3 |
| 3PVM-B | 34.9 | 5.8 | Complement C5 |
| 7S63-A | 31.8 | 5.6 | Alpha 2-macroglobulin |
| 4LNV-A | 27.3 | 7.0 | Thioester-containing protein I |
| 4RTD-A | 18.8 | 9.2 | Uncharacterized lipoprotein Yfhm |
| 5A42-A | 18.3 | 8.2 | Uncharacterized lipoprotein Yfhm |
| 2SQC-A | 14.3 | 13.6 | Squalene-hopene cyclase |
| 3PMM-A | 13.1 | 3.3 | Putative cytoplasmic protein |
| 4V1R-A | 12.9 | 3.4 | Alpha-1,6-mannanase |
References
[1] Interaction of C5 protein with RNA aptamers selected by SELEX.Lee, J. H., Kim, H., Ko, J., & Lee, Y.
Nucleic acids research, 30(24), 5360–5368. (2002)