Hi Guillaume, Regarding your suggested experiment, something similar is presented in Supplementary Video 2 in the following paper: https://www.nature.com/articles/s41586-020-2829-0
Best wishes, Tomas On Mon, Mar 17, 2025 at 4:03 PM Guillaume Gaullier <guillaume.gaull...@kemi.uu.se> wrote: > > Hello, > > > Sorry to hijack this discussion, but does someone know if reduction of a > disulphide could be a manifestation of radiation damage? Especially in > cryoEM, since we're shooting electrons at it. > > > One way to test this would be to do a rough zero-dose extrapolation (repeat > motion correction with fewer and fewer frames, use the particle coordinates > and orientations determined with the full dose to extract particle images and > do reconstructions from the micrographs obtained with fewer frames) and see > if this feature appears with accumulated dose. But this is tricky to do if > motion correction is not perfect. At least according to the paper that > introduced HexAuFoil grids: https://doi.org/10.1126/science.abb7927 ; but I > don't know if anyone has tried even without these grids. > > > Cheers, > > > Guillaume > > ________________________________ > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Artem > Evdokimov <artem.evdoki...@gmail.com> > Sent: Monday, March 17, 2025 4:50:37 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Query Regarding Additional Density Near Disulfide Bond > in Cryo-EM Structure > > To me this looks like a mixture of oxidized and reduced states of the S-S > bond. Hard to say with any certainty seeing as the (optical) resolution is > modest. > > Artem > > - Cosmic Cats approve of this message > > > On Mon, Mar 17, 2025 at 8:18 AM Devbrat Kumar <devformed...@gmail.com> wrote: >> >> Hello Everyone, >> >> I am worried about the density of the disulfide bond in the cryo-EM >> structure that I am analyzing. The experimental map shows the expected >> density for the disulfide bond involving two cysteine residues, but in >> addition, I see some unexplained density, which I do not know how to >> interpret. >> >> I have attached the figure for your reference. Does anyone have experience >> with such extra density around a disulfide bond in their structures? Any >> thoughts would be greatly appreciated. >> >> Thanks for your attention and assistance. >> >> Warm regards >> Devbrat kumar >> Postdoctoral Fellow >> IITD, In >> >> ________________________________ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen > avsändaren och vet att innehållet är säkert. > CAUTION: Do not click on links or open attachments unless you recognise the > sender and know the content is safe. > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär det > att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan > du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal data. > For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
