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

[r.fronzes at iecb.u-bordeaux.fr]

Dear Alexander, Dear All, 

We have seen the same type of non-identified density in some of our maps. Very dense pyramidal density with a similar binding site.
So far, we could not identify it. So we are also very interested by any hints !!!
To us, the high density points towards a metal (Fe, Zn, …) complexed in some larger structure….

Many thanks

All the best

Rémi


Rémi Fronzes, PhD

Group Leader Institut Européen de Chimie et Biologie
Directeur de recherche CNRS 

UMR 5234 CNRS/université de Bordeaux 
Microbiologie Fondamentale et Pathogénicité (MFP)

IECB - Univ. Bordeaux
2 rue Robert Escarpit, 
33607 Pessac, France
Rémi Fronzes, PhD

Group Leader Institut Européen de Chimie et Biologie
Directeur de recherche CNRS 

UMR 5234 CNRS/université de Bordeaux 
Microbiologie Fondamentale et Pathogénicité (MFP)

IECB - Univ. Bordeaux
2 rue Robert Escarpit, 
33607 Pessac, France


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> Le 17 janv. 2023 à 11:17, Dr. Alexander Belyy <alexander.belyy at mpi-dortmund.mpg.de> a écrit :
> 
> 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
> <MysteriousDensity.jpg>_______________________________________________
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