[3dem] Antw: Re: [ext] Re: A strong density in the cryo-EM map
Sharon G Wolf
Sharon.Wolf at weizmann.ac.il
Tue Jan 17 06:15:51 PST 2023
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>_______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>
>>
>>
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>>
>
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
More information about the 3dem
mailing list