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Complement component 5 aptamer
Description
Lee, Y. et al. reported aptamers with affinity for complement component 5 in their article published in 2002. The W2 aptamer was named by Lee, Y. et al. in the article[1].
SELEX
In their work published in 2002, Lee, Y. 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. C5 protein was expressed in E. coli as a fusion with maltose-binding protein.[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. The structure of this aptamer is relatively simple, consisting of only one stem loop with one bulge. The 5' and 3' ends of aptamer each has an overhang[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. Derived from proteolytic degradation of complement C5, C5a anaphylatoxin is a mediator of local inflammatory process. Binding to the receptor C5AR1 induces a variety of responses including intracellular calcium release, contraction of smooth muscle, increased vascular permeability, and histamine release from mast cells and basophilic leukocytes.-----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 |
|---|---|---|---|---|---|---|
| C5 protein | P01031 | PF07678 | 188.305 kDa |
......
MGLLGILCFLIFLGKTWGQEQTYVISAPKIFRVGASENIVIQVYGYTEAFDATISIKSYPDKKFSYSSGHVHLSSENKFQNSAILTIQPKQLPGGQNPVSYVYLEVVSKHFSKSKRMPITYDNGFLFIHTDKPVYTPDQSVKVRVYSLNDDLKPAKRETVLTFIDPEGSEVDMVEEIDHIGIISFPDFKIPSNPRYGMWTIKAKYKEDFSTTGTAYFEVKEYVLPHFSVSIEPEYNFIGYKNFKNFEITIKARYFYNKVVTEADVYITFGIREDLKDDQKEMMQTAMQNTMLINGIAQVTFDSETAVKELSYYSLEDLNNKYLYIAVTVIESTGGFSEEAEIPGIKYVLSPYKLNLVATPLFLKPGIPYPIKVQVKDSLDQLVGGVPVTLNAQTIDVNQETSDLDPSKSVTRVDDGVASFVLNLPSGVTVLEFNVKTDAPDLPEENQAREGYRAIAYSSLSQSYLYIDWTDNHKALLVGEHLNIIVTPKSPYIDKITHYNYLILSKGKIIHFGTREKFSDASYQSINIPVTQNMVPSSRLLVYYIVTGEQTAELVSDSVWLNIEEKCGNQLQVHLSPDADAYSPGQTVSLNMATGMDSWVALAAVDSAVYGVQRGAKKPLERVFQFLEKSDLGCGAGGGLNNANVFHLAGLTFLTNANADDSQENDEPCKEILRPRRTLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVASQLRANISHKDMQLGRLHMKTLLPVSKPEIRSYFPESWLWEVHLVPRRKQLQFALPDSLTTWEIQGVGISNTGICVADTVKAKVFKDVFLEMNIPYSVVRGEQIQLKGTVYNYRTSGMQFCVKMSAVEGICTSESPVIDHQGTKSSKCVRQKVEGSSSHLVTFTVLPLEIGLHNINFSLETWFGKEILVKTLRVVPEGVKRESYSGVTLDPRGIYGTISRRKEFPYRIPLDLVPKTEIKRILSVKGLLVGEILSAVLSQEGINILTHLPKGSAEAELMSVVPVFYVFHYLETGNHWNIFHSDPLIEKQKLKKKLKEGMLSIMSYRNADYSYSVWKGGSASTWLTAFALRVLGQVNKYVEQNQNSICNSLLWLVENYQLDNGSFKENSQYQPIKLQGTLPVEARENSLYLTAFTVIGIRKAFDICPLVKIDTALIKADNFLLENTLPAQSTFTLAISAYALSLGDKTHPQFRSIVSALKREALVKGNPPIYRFWKDNLQHKDSSVPNTGTARMVETTAYALLTSLNLKDINYVNPVIKWLSEEQRYGGGFYSTQDTINAIEGLTEYSLLVKQLRLSMDIDVSYKHKGALHNYKMTDKNFLGRPVEVLLNDDLIVSTGFGSGLATVHVTTVVHKTSTSEEVCSFYLKIDTQDIEASHYRGYGNSDYKRIVACASYKPSREESSSGSSHAVMDISLPTGISANEEDLKALVEGVDQLFTDYQIKDGHVILQLNSIPSSDFLCVRFRIFELFEVGFLSPATFTVYEYHRPDKQCTMFYSTSNIKIQKVCEGAACKCVEADCGQMQEELDLTISAETRKQTACKPEIAYAYKVSITSITVENVFVKYKATLLDIYKTGEAVAEKDSEITFIKKVTCTNAELVKGRQYLIMGKEALQIKYNFSFRYIYPLDSLTWIEYWPRDTTCSSCQAFLANLDEFAEDIFLNGC
|
3CU7 | 727 |
Some isolated sequences bind to the affinity of the protein[1].
| 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(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 |
|---|---|---|---|
| 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)