iCn3D Tutorial: Overlay many ACE2 receptor binding domain analogous to SARS-Co2 RBD using Blast
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Use BlastP to align receptor-binding domains
PDB ID: 6M0J
- SARS-CoV-2 spike receptor-binding domain bound with ACE2
- Angiotensin-converting enzyme 2, chain A, denoted 6M0J_A, pink
- Spike Protein S1, chain B, denoted 6M0J_E, blue
Instructions
- File, Retrieve by ID, MMDB
- Seq. & Annotations. In Summary tab check Custom and Conserved Domains
- In Summary tab, click on 6M0J_E
- View, View Selection
- In Details tab, Add track.
- Choose the FASTA Alignment Tab in the new window
- Cut and paste the aligned FASTA sequences file you made using the instructions on the next page or to save time just copy/paste the same FASTA Alignment file below into the iCn3D Fasta window.
- Enter 319 for the Position of the first residue in Sequences & Annotations window (# is right there); Check Color sequence by identity:
- Choose Add Tracks. The RBD appears color coded with the darkest rd 100% identity and the darkest blue 0% (See F377, K387)
- Style, Background, White
- File, Share Link, Lifelong Short Link (this might not work if you choose too many proteins)
Instructions to use Blast
Use of BlastP for COV-2 ACE2 Receptor Binding Domain (RBD)
Find sequences homologous to the structure of the RBSthrough BlastP:
Instructions - use this image for help
- Go to BlastP
- Enter this Accession number (in this case PDB ID with chain: 6M0J_E for the RBD
- Under Choose Search Set
- Database: Choose UniProt
- Organism: input Coronavirus and click it when it appears in the search
- Add Organism and then input SARS-CoV-2 and click it when it appears in the search; Click Exclude (since we already know the structure of the RBD of CoV-2)
- Choose Blastp and then BLAST
- After a few minutes you will get the general output shown below .
- Check just the ones with percent identity >30% and choose Download, Fasta Aligned Sequences
- Copy the resulting text file and use in iCn3D as described in the previous page.