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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Dear Alexander and Rémi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">did you ever measure UV-Vis or Excitation spectra of your proteins, to get some spectroscopic information on the bound cluster?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">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”)?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">A bit more information would be helpful – you could also send them in an individual email.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Magdalena<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:black">------------------------------------------------------------------------------------------------</span><span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Magdalena Schacherl, PhD</span><span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Group Leader Structural Enzymology</span><span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Charité - Universitätsmedizin Berlin</span><span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Institute of Medical Physics and Biophysics | Charitéplatz 1 | 10117 Berlin</span><span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Internal address: Virchowweg 6 Room 03.322, level 3</span><span lang="EN-US" style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">T: +49 30 450 524196 | F: +49 30 450 524952</span><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><a href="mailto:magdalena.schacherl@charite.de" title="mailto:magdalena.schacherl@charite.de"><span style="color:black">magdalena.schacherl@charite.de</span></a></span><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> </span><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><a href="https://urldefense.com/v3/__https://biophysik.charite.de/en/research/structural_enzymology/__;!!Mih3wA!G1w8c_FrzvLWzceNy-t7E4DhjKlnSzWviw3d16mO6j1s6g02DvtU8_7HUKl1Z1Ti-NCEc2ZzyVjuAV1VJuTh_icltfs7r7Oh$" title="https://biophysik.charite.de/en/research/structural_enzymology/"><span style="color:black">Website Schacherl lab</span></a></span><span style="font-size:13.5pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">Von: </span></b><span style="font-size:12.0pt;color:black">3dem <3dem-bounces@ncmir.ucsd.edu> im Auftrag von "r.fronzes@iecb.u-bordeaux.fr" <r.fronzes@iecb.u-bordeaux.fr><br>
<b>Datum: </b>Dienstag, 17. Januar 2023 um 12:22<br>
<b>An: </b>"Dr. Alexander Belyy" <alexander.belyy@mpi-dortmund.mpg.de><br>
<b>Cc: </b>"3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
<b>Betreff: </b>[ext] Re: [3dem] A strong density in the cryo-EM map<o:p></o:p></span></p>
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<p class="MsoNormal">Dear Alexander, Dear All, <o:p></o:p></p>
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<p class="MsoNormal">We have seen the same type of non-identified density in some of our maps. Very dense pyramidal density with a similar binding site.<o:p></o:p></p>
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<p class="MsoNormal">So far, we could not identify it. So we are also very interested by any hints !!!<o:p></o:p></p>
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<p class="MsoNormal">To us, the high density points towards a metal (Fe, Zn, …) complexed in some larger structure….<o:p></o:p></p>
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<p class="MsoNormal">Many thanks<o:p></o:p></p>
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<p class="MsoNormal">All the best<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Rémi<o:p></o:p></p>
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<p class="MsoNormal">Rémi Fronzes, PhD<br>
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Group Leader Institut Européen de Chimie et Biologie<br>
Directeur de recherche CNRS <br>
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UMR 5234 CNRS/université de Bordeaux <br>
Microbiologie Fondamentale et Pathogénicité (MFP)<br>
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IECB - Univ. Bordeaux<br>
2 rue Robert Escarpit, <br>
33607 Pessac, France<o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">Rémi Fronzes, PhD<br>
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Group Leader Institut Européen de Chimie et Biologie<br>
Directeur de recherche CNRS <br>
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UMR 5234 CNRS/université de Bordeaux <br>
Microbiologie Fondamentale et Pathogénicité (MFP)<br>
<br>
IECB - Univ. Bordeaux<br>
2 rue Robert Escarpit, <br>
33607 Pessac, France<br>
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<i>I don’t expect you to read or respond to my email outside your work hours.<br>
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Je ne m'attends pas à ce que vous lisiez ou répondiez à mon courrier électronique en dehors de vos heures de travail.</i><br>
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<p class="MsoNormal">Le 17 janv. 2023 à 11:17, Dr. Alexander Belyy <alexander.belyy@mpi-dortmund.mpg.de> a écrit :<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Dear community of structural biologists,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><br>
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?).<br>
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We would be grateful for any suggestions as to what this might be.<br>
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Thank you!<br>
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Best regards from Dortmund,<br>
Alexander<o:p></o:p></span></p>
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<p class="MsoNormal"><MysteriousDensity.jpg><span style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
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