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Biology LibreTexts

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

  1. File, Retrieve by ID, MMDB
  2. Seq. & Annotations. In Summary tab check Custom and Conserved Domains
  3. In Summary  tab, click on 6M0J_E
  4. View, View Selection
  5. In Details tab, Add track.
  6. Choose the FASTA Alignment Tab in the new window
  7. 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.
  8. Enter 319 for the Position of the first residue in Sequences & Annotations window (# is right there);  Check Color sequence by identity:
  9. Choose Add Tracks.  The RBD appears color coded with the darkest rd 100% identity and the darkest blue 0% (See F377, K387)
  10. Style, Background, White
  11. 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

clipboard_e976c47cc8026cf6e00f0f19d96063350.png

  1. Go to BlastP
  2. Enter this Accession number (in this case PDB ID with chain:  6M0J_E for the RBD
  3. Under Choose Search Set
  4. Database:  Choose UniProt
  5. Organism:  input Coronavirus and click it when it appears in the search
  6. 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)  
  7. Choose Blastp and then BLAST
  8. After a few minutes you will get the general output shown below . 

    clipboard_e2b1853b03965634adca18762dcd4e682.png
  9. Check just the ones with percent identity >30% and choose Download, Fasta Aligned  Sequences
  10. Copy the resulting text file and use in iCn3D as described in the previous page.

iCn3D Tutorial: Overlay many ACE2 receptor binding domain analogous to SARS-Co2 RBD using Blast is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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