[3dem] Membrane protein structure: orientation issue

[Jacopo Marino]

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
>
>
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-- 
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

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