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

[Christian Tüting]

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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