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Make A Structure Alignment Within Cn3D

  Sample User Question
Flow Chart
Step By Step Guide

Sample User Question back to top

View a structural alignment of the human Leptin protein (MMDB: 9153; PDB: 1AX8) with the human Ciliary Neurotrophic Factor protein (MMDB: 5903; PDB: 1CNT). Look at the similarities and differences between these two proteins. Can you add the structure for human prolactin (MMDB: 22679; PDB: 1N9D) to the alignment?

Analysis/Comments back to top

A structural alignment is based on similarities in 3-dimensional form rather than linear sequence. As such, it is a much more complicated alignment and requires more extensive computing power. This is why the structure alignments are precalculated and stored for retrieval instead of being generated upon user demand like sequence alignments.

Flow Chart back to top

  1. NCBI Entrez Structure Division - Search MMDB using standard Entrez searching techniques.

  2. Cn3D - This molecular viewer program will display structural alignments. It should be pre-installed.

Step By Step Guide back to top

Entrez Structure

  • Locate the structure summary for the human Leptin protein (PDB: 1AX8).
  • View the structure using Cn3D.

  • From the Sequence Window's Imports Menu select "Show Imports." This will open the Import Window.
  • From the Import Window's Edit Menu, select "Import Structures." From the dialog box that opens up, select "Via Network."
  • Enter the MMDB identifier number for human Ciliary Neurotrophic Factor protein (MMDB: 5903).
  • Select to align to chain 1.
  • It will create an alignment in the Import Window, but also it will provide a warning that is is necessary to save the alignment to a file and then re-open it in Cn3D. Click on "OK."
  • From the Import Window's Alignment Menu, select either "Merge Single" or "Merge All" depending on how many structures have been imported. Click on the alignment when the cursor turns to a "+".
  • Close the Import Window.
  • From the Structure Window's File Menu, select "Save." Give it a file name and say "yes" to any queries.
  • From the Structure Window's File Menu, select "Open." Choose the file that was just saved.
  • It should open in Cn3D and show the structural alignment.
  • This process can be repeated to add other structure to the alignment.

Structures Return to Slides (*.html or *.mht format)
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Revised 08/08/2007