[3dem] Membrane protein structure: orientation issue

[Philip Köck]

​Why do you say that the symmetry has to be at least C3?

All the best,

Philip



Från: 3dem <3dem-bounces at ncmir.ucsd.edu> för Dmitry Lyumkis <dlyumkis at salk.edu>
Skickat: den 25 mars 2020 07:07
Till: Jacopo Marino
Kopia: 3dem at ncmir.ucsd.edu
Ämne: Re: [3dem] Membrane protein structure: orientation issue
  
Assuming this is a symmetric membrane protein with at least 3-fold rotational symmetry, you don’t need the top and bottom views to fully sample Fourier space and arrive at a high-quality reconstruction. Side-views of a rotationally symmetric particle are  sufficient, and the reconstruction will be complete. 






Dmitry Lyumkis
Assistant Professor
The Salk Institute for Biological Studies
10010 North Torrey Pines Road, La Jolla, CA 92037
T: 858-453-4100 x1155
E: dlyumkis at salk.edu
https://lyumkis.salk.edu



 





On Mar 24, 2020, at 10:53 PM, Jacopo Marino <jacopo.marino at psi.ch> wrote:


How much do you really need top and bottom views for 3D reconstruction ? Have you tried ?


On 25.03.2020 06:48, Saumya Verma Bajaj wrote:
 

Dear all, 

I am trying to solve the structure of a tetrameric membrane protein complex, with the protein embedded in detergent micelle (0.05% GDN) and a soluble accessory protein attached to it.  

Following 2D classification, while the side views and oblique views are easily visible, and the top/bottom are very few (~1-2%) (please see attached image) and get further diminished in subsequent rounds of 2D classification.     

While we are trying different grid types to overcome the orientation problem at the sample level, I was wondering if there are certain tweaks we can make to the analysis parameters (particle picking, box size, mask, ctf  etc.) to enhance the signal of protein embedded within a micelle in the current data set. We are using Relion3.1 for SPA. 

Any suggestions to salvage this set of data will be very helpful. 

Thank you.
Best regards,
Saumya 
_______________________________________________ 3dem mailing list 3dem at ncmir.ucsd.edu https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem  --  Dr. Jacopo Marino Laboratory of Biomolecular Research Paul Scherrer Institute OFLB/005 5232 Villigen PSI, Switzerland tel: +41 56 310 5484 (or +41 56 310 5777) e-mail: jacopo.marino at psi.ch    _______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem