[3dem] A strong density in the cryo-EM map

[Matthias Wolf]

Hi Alex,

Too small and too thick for porphyrin.
It looks octahedral.
Surrounded by pos charged AA.
Complex 6-coordinated metal ion?
https://urldefense.com/v3/__https://www.chemguide.co.uk/inorganic/complexions/shapes.html__;!!Mih3wA!HJjVr4vJXKxksPZjaBBP7djvCXQffkeVWEEoIdQk82u6WnSQlY5FrbGJEQMP3jAic8DXJhfvdpSt44ojLbtyV4TAn3s$ 
AlF6?

Can you get rid of it with EDTA?
Use ICP-MS to identify!

Good luck,
   Matthias
________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Dr. Alexander Belyy <alexander.belyy at mpi-dortmund.mpg.de>
Sent: Tuesday, January 17, 2023 7:17:25 PM
To: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Subject: [3dem] A strong density in the cryo-EM map


Dear community of structural biologists,

In a 3.5 Å cryo-EM reconstruction, we have discovered a large density of 10-12 Å diameter that we are having difficulty identifying (see attachment). This density is surrounded by 5 arginines, 3 asparagines, 2 glutamines, 1 aspartate, and 1 glutamate coming from 4 different regions of the protein. Functionally, the density is needed to hold the protein together. This density appears at higher thresholds than the protein itself and is visible even at the 2D class level. After local refinement and sharpening, the density becomes pyramid-like with a series of smaller spheres with pseudosymmetry (or C3?).

We would be grateful for any suggestions as to what this might be.

Thank you!

Best regards from Dortmund,
Alexander
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