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

[Schacherl, Magdalena]

Dear Alexander and Rémi,

did you ever measure UV-Vis or Excitation spectra of your proteins, to get some spectroscopic information on the bound cluster?

What kind of protein class is it? Are you sure about the modelling of the protein part (identity of the side chains at the “cluster”)?
A bit more information would be helpful – you could also send them in an individual email.

Best regards,
Magdalena


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Magdalena Schacherl, PhD
Group Leader Structural Enzymology
Charité - Universitätsmedizin Berlin
Institute of Medical Physics and Biophysics  | Charitéplatz 1 | 10117 Berlin
Internal address: Virchowweg 6 Room 03.322, level 3
T: +49 30 450 524196 | F: +49 30 450 524952
magdalena.schacherl at charite.de<mailto:magdalena.schacherl at charite.de>

Website Schacherl lab<https://urldefense.com/v3/__https://biophysik.charite.de/en/research/structural_enzymology/__;!!Mih3wA!G1w8c_FrzvLWzceNy-t7E4DhjKlnSzWviw3d16mO6j1s6g02DvtU8_7HUKl1Z1Ti-NCEc2ZzyVjuAV1VJuTh_icltfs7r7Oh$ >



Von: 3dem <3dem-bounces at ncmir.ucsd.edu> im Auftrag von "r.fronzes at iecb.u-bordeaux.fr" <r.fronzes at iecb.u-bordeaux.fr>
Datum: Dienstag, 17. Januar 2023 um 12:22
An: "Dr. Alexander Belyy" <alexander.belyy at mpi-dortmund.mpg.de>
Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
Betreff: [ext] Re: [3dem] A strong density in the cryo-EM map

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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