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

[Sharon G Wolf]

As Jaime said, you could try elemental analysis with TEM-EDX. Cryo or dry. It may be below the detection limit but it is worth a try. Try  at RT with a light stain and it might work.

Sent from my iPhone

> On 17 Jan 2023, at 14:35, Christian Tüting <christian.tueting at biochemtech.uni-halle.de> wrote:
> 
> Hi all,
> 
> you can try to run AlphaFill on your pdb structure. This algorithm is
> trained to identify binding sites and "transplant" ligands.
> Maybe, your ligand is already known, and the binding site could be
> recognized by the algorithm.
> 
> If you get a hit, you can easily design an experiment to prove this.
> 
> Compared to experimental approaches, this is very easy to do.
> 
> Best
> Christian
> 
> 
>>>> Jaime Llodra <jaimellodra at gmail.com> 17.01.23 13.18 Uhr >>>
> Dear All,
> Is it possible to do elemental analysis to have an idea of elements
> present
> in this purified protein?
> 
> Best,
> 
> Jaime Llodrá
> 
>> On Tue, Jan 17, 2023 at 11:59 AM Schacherl, Magdalena <
>> magdalena.schacherl at charite.de> wrote:
>> 
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> ------------------------------------------------------------------------------------------------
>> 
>> 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
>> 
>> 
>> 
>> 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
>> 
>> 
>> ————————————————————————————————
>> 
>> 
>> 
>> *I don’t expect you to read or respond to my email outside your work
>> hours. Je ne m'attends pas à ce que vous lisiez ou répondiez à mon
> courrier
>> électronique en dehors de vos heures de travail.*
>> 
>> 
>> 
>> 
>> 
>> 
>> 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 gluta> 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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