Question about viewing 3D protein structure

Dear List members,

I would like to view the 3D structure of a gene that we cloned and sequenced. We translated the sequence to amino acids. I saw that you can right click on the sequence and then “3D structure data” pops up. I entered the PDB ID of a gene that is similar, but found in another organism. I was wondering if this 3D structure that is shown is the sequence that I entered from our work based on the PDB ID that I entered or is it simply the 3D structure of the PDB ID that I entered?

Thanks so much for your time and help. I always recommend this program for so many uses!

Regards,

Mollee Crampton, M.S.
Research Technician: Molecular Genetics & EpiGenomics
Delaware State University
Phone: 302-857-6461

Hi Mollee … this is a good question !

I would like to view the 3D structure of a gene that we cloned and sequenced. We translated the sequence to amino acids. I saw that you can right click on the sequence and then “3D structure data” pops up. I entered the PDB ID of a gene that is similar, but found in another organism. I was wondering if this 3D structure that is shown is the sequence that I entered from our work based on the PDB ID that I entered or is it simply the 3D structure of the PDB ID that I entered?

The structure is that of the PDB ID you entered. However, the colouring is transferred onto the structure based on a conservative alignment between the sequence extracted from the PDB structure coordinates, and the sequence from your work. You can see the alignment via the File->View mappings option in the structure window, and you’ll be able to see any mismatches or unmatched structure data as grey patches on the 3D structure.

If you want to explore the likely structure of your sequence I’d recommend the Swissmodel or Phyre2 servers as a good place to start. You can load the models generated by these servers directly onto the sequence and view it in Jalview. Let us know if you have any questions!

Happy modelling!
Jim.

···

On 18/11/2015 18:33, Mollee Crampton wrote:

Hello Jim,

Thank you so much for responding quickly. I appreciate your suggestions and am trying Swissmodel now.

Have a great day,

···

Mollee Crampton, M.S.
Research Technician: Molecular Genetics & EpiGenomics
Delaware State University
Phone: 302-857-6461

From: Jim Procter [mailto:foreveremain@gmail.com] On Behalf Of Jim Procter
Sent: Wednesday, November 18, 2015 3:03 PM
To: Mollee Crampton
Cc: jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Question about viewing 3D protein structure

Hi Mollee … this is a good question !

On 18/11/2015 18:33, Mollee Crampton wrote:

I would like to view the 3D structure of a gene that we cloned and sequenced. We translated the sequence to amino acids. I saw that you can right click on the sequence and then “3D structure data” pops up. I entered the PDB ID of a gene that is similar, but found in another organism. I was wondering if this 3D structure that is shown is the sequence that I entered from our work based on the PDB ID that I entered or is it simply the 3D structure of the PDB ID that I entered?

The structure is that of the PDB ID you entered. However, the colouring is transferred onto the structure based on a conservative alignment between the sequence extracted from the PDB structure coordinates, and the sequence from your work. You can see the alignment via the File->View mappings option in the structure window, and you’ll be able to see any mismatches or unmatched structure data as grey patches on the 3D structure.

If you want to explore the likely structure of your sequence I’d recommend the Swissmodel or Phyre2 servers as a good place to start. You can load the models generated by these servers directly onto the sequence and view it in Jalview. Let us know if you have any questions!

Happy modelling!
Jim.