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jobRxivPhD student in cryo-ET of membrane trafficking at MPI-NAT in Göttingen, DE Max-Planck-Institute for Multidisciplinary Science Join our <a href="https://mas.to/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> lab at MPI-NAT in Göttingen for a PhD in membrane traffickingSee the full job description on jobRxiv: <a href="https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778</a>... <a href="https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-phd-student-in-cryo-et-of-membrane-trafficking-at-mpi-nat-in-gottingen-de/?fsp_sid=914" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-phd-student-in-cryo-et-of-membrane-trafficking-at-mpi-nat-in-gottingen-de/?fsp_sid=914</a>

SBGridMeharry Medical College Ph.D. candidate KeAndreya Morrison's highlight features a <a href="https://mstdn.social/@Nature" class="u-url mention">@Nature</a> Communications publication from the laboratory of Christopher D. Lima whose work helped to uncover how the cell’s nuclear gateway controls molecular traffic and regulate protein function, offering new insights into gene regulation and disease.Read more here: <a href="https://medium.com/sbgrid-community-news/dual-role-of-the-nuclear-gatekeeper-47013dcb1b05" target="_blank" rel="nofollow noopener noreferrer" translate="no">https://medium.com/sbgrid-community-news/dual-role-of-the-nuclear-gatekeeper-47013dcb1b05</a><a href="https://mstdn.science/tags/SBGrid" class="mention hashtag" rel="tag">#SBGrid</a> <a href="https://mstdn.science/tags/CryoEM" class="mention hashtag" rel="tag">#CryoEM</a> <a href="https://mstdn.science/tags/StructuralBiology" class="mention hashtag" rel="tag">#StructuralBiology</a>

jobRxivPhD student in cryo-ET of membrane trafficking at MPI-NAT in Göttingen, DE Max-Planck-Institute for Multidisciplinary Science Join our <a href="https://mas.to/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> lab at MPI-NAT in Göttingen for a PhD in membrane traffickingSee the full job description on jobRxiv: <a href="https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778</a>... <a href="https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-phd-student-in-cryo-et-of-membrane-trafficking-at-mpi-nat-in-gottingen-de/?fsp_sid=487" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/max-planck-institute-for-multidisciplinary-science-27778-phd-student-in-cryo-et-of-membrane-trafficking-at-mpi-nat-in-gottingen-de/?fsp_sid=487</a>

Guillaume GaullierOh, a new homemade time-resolved vitrification device for <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> !<a href="https://doi.org/10.1101/2025.07.22.666177" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1101/2025.07.22.666177</a>Shake-it-up + Back-it-up = Mix-it-up

StructBiolCommunicationsThis study of imidazole glycerol phosphate dehydratase suggests that cryo-EM can be useful in pinpointing the mode of binding small molecules of low mass and mapping protein-ligand interactions <a href="https://mstdn.science/tags/CryoEM" class="mention hashtag" rel="tag">#CryoEM</a> <a href="https://mstdn.science/tags/Tuberculosis" class="mention hashtag" rel="tag">#Tuberculosis</a> <a href="https://mstdn.science/tags/HistidineBiosynthesisPathway" class="mention hashtag" rel="tag">#HistidineBiosynthesisPathway</a> <a href="https://doi.org/10.1107/S2053230X25004595" target="_blank" rel="nofollow noopener noreferrer" translate="no">https://doi.org/10.1107/S2053230X25004595</a>

Keiran RowellStructure of an archaeal ribosome reveals a divergent active site and hibernation factor | Nature Micro<a href="https://rdcu.be/ewZ3S" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://rdcu.be/ewZ3S</a>"Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase centre (PTC) is thought to be nearly universally conserved. Here we identify clades of archaea that have highly divergent ribosomal RNA sequences in the PTC."<a href="https://mastodon.social/tags/archea" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#archea</a> <a href="https://mastodon.social/tags/structuralbiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structuralbiology</a> <a href="https://mastodon.social/tags/ribosome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ribosome</a> <a href="https://mastodon.social/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a>

Guillaume GaullierLooks like I accidentally started an <a href="https://fediscience.org/tags/FSCFriday" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#FSCFriday</a> on CCPEM... 🤭 😅<a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> <a href="https://fediscience.org/tags/Oops" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Oops</a>

PLOS BiologyThe <a href="https://fediscience.org/tags/macrophage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#macrophage</a> CD163 receptor clears free <a href="https://fediscience.org/tags/hemoglobin" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#hemoglobin</a> in the bloodstream by binding the HpHb complex. The <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> structure of CD163-HpHb complex, by <a href="https://mstdn.science/@chingshinhuang" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@chingshinhuang</a> &co, reveals how CD163-mediated endocytosis clears different HpHb isoforms <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@PLOSBiology</a> <a href="https://plos.io/4nNBbGI" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://plos.io/4nNBbGI</a>

eLife🧪 C. thermocellum is a biofuel workhorse, but its ethanol yield still falls short.A new <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> structure of its key enzyme, AdhE, shows how the microbe safely handles harmful by-products and keeps its internal chemistry in balance. <a href="https://elifesciences.org/articles/96966?utm_source=mastodon&utm_medium=social&utm_campaign=organic" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://elifesciences.org/articles/96966?utm_source=mastodon&utm_medium=social&utm_campaign=organic</a>

François Ferron 🇪🇺 🔷️🔶️The major 🇨🇵 structural biology event of 2025 co-organized with the Association Française de Cristallographie (<a href="https://fediscience.org/tags/AFC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AFC</a>) and the Société Française de Biophysique (<a href="https://fediscience.org/tags/SFB" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SFB</a>) is coming : <a href="https://fediscience.org/tags/BSI4" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#BSI4</a> | 4th edition of the Integrative Structural Biology Meeting (BSI), 15-19 December 2025, <a href="https://fediscience.org/tags/Bordeaux" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bordeaux</a>, France more information ➡️ <a href="https://bsi4.org/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://bsi4.org/</a> <a href="https://bsky.brid.gy/r/https://bsky.app/profile/afmblab.bsky.social" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@afmblab.bsky.social</a> <a href="https://a.gup.pe/u/strucbio" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@strucbio</a> <a href="https://mstdn.science/@ActaCrystF" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@ActaCrystF</a> <a href="https://sciencemastodon.com/@sciencemagazine" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@sciencemagazine</a> <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@PLOSBiology</a> <a href="https://fediscience.org/tags/biophysics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biophysics</a> <a href="https://fediscience.org/tags/crystalography" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#crystalography</a> <a href="https://fediscience.org/tags/SAXS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SAXS</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

Keiran RowellIn situ structure of a bacterial flagellar motor at subnanometre resolution reveals adaptations for increased torque | Nature Microbiology<a href="https://www.nature.com/articles/s41564-025-02012-9" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.nature.com/articles/s41564-025-02012-9</a><a href="https://mastodon.social/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> <a href="https://mastodon.social/tags/evolution" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#evolution</a> <a href="https://mastodon.social/tags/bacteria" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bacteria</a> <a href="https://mastodon.social/tags/flagella" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#flagella</a> <a href="https://mastodon.social/tags/motor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#motor</a>

PLOS Biology<a href="https://fediscience.org/tags/Glycoprotein" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Glycoprotein</a> 2 (GP2) filaments protect against infections by acting as decoys for the bacterial <a href="https://fediscience.org/tags/lectin" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#lectin</a> FimH. The <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> structure of GP2 filaments provides insights into filament assembly and <a href="https://fediscience.org/tags/antibacterial" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#antibacterial</a> function in the digestive tract <a href="https://fediscience.org/@PLOSBiology" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@PLOSBiology</a> <a href="https://plos.io/3HP2obF" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://plos.io/3HP2obF</a>

Guillaume GaullierAn interesting use case of LLMs is as a conversational interface to some body of text, as a complement to other forms of navigation: from a table of content or index, via full-text search, or reading specific sections or even the whole text cover-to-cover.Of course the LLM can still make up nonsense, but this is a similar limitation to a full-text search leading to a section irrelevant to your current question if the search terms match too broadly. With any navigation method, eventually you need to read the material, once you find the section you need.The Phenix documentation, papers, newsletters and tutorial videos have been fed to an LLM, so now we can navigate it as a conversation: <a href="https://phenix-online.org/version_docs/2.0-5725/reference/chatbot.html" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://phenix-online.org/version_docs/2.0-5725/reference/chatbot.html</a> A quick test trying to answer a question I knew the answer to suggests that it is working pretty well for sufficiently specific questions. This will likely be useful.<a href="https://fediscience.org/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://fediscience.org/tags/crystallography" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#crystallography</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

Guillaume GaullierToday was the last day of a practical course on <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> for PhD students that I helped teaching (first time for me, but this was the 3rd or 4th edition of the course). It was a lot of fun! ❄️ 🔬 🤓It is an ambitious course. A few lectures about the theory, then mostly practicals all the way: vitrification, screening, more vitrification if needed, data collection, image processing. With seminars at key steps, for the students to discuss their progress and plan their next steps. We provide backup samples if necessary, but it is intended to primarily use samples provided by the students. And wow did they bring challenging things this year! Floppy RNA, tiny proteins; stuff far beyond the difficulty of the average tutorial dataset. 🤯Even as one of the teachers, I also learned a few things during this course:- New ways in which grid handling and vitrification can be challenging. I had to rescue some strange cases during the vitrification practicals. It's good practice, keeps these fine motor skills sharp. 🙃 - ApoF is a really weird particle, and in my opinion not the best one to learn image processing with. Believe it or not, this course was my first time processing an ApoF dataset.I really hope the course runs again next year and I get to teach in it again.

Guillaume GaullierWhen depositing <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> data to <a href="https://fediscience.org/tags/EMPIAR" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#EMPIAR</a>, I can never remember how to determine the "voxel type" requested in the metadata entry form.Over the years, I have asked about it on CCPEM, bookmarked the permalink to the answer I received back then (probably in multiple browser profiles) and written similar notes at different places in my system.Here is one more note about it, this time public: <a href="https://www.gaullier.org/en/blog/2025/06/01/voxel-type-empiar-deposition/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.gaullier.org/en/blog/2025/06/01/voxel-type-empiar-deposition/</a>

eLifeA new method called MagIC-Cryo-EM allows scientists to use powerful <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> techniques to examine proteins that have been difficult to study so far. <a href="https://elifesciences.org/digests/103486/the-molecular-shape-of-you?utm_source=mastodon&utm_medium=social&utm_campaign=organic" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://elifesciences.org/digests/103486/the-molecular-shape-of-you?utm_source=mastodon&utm_medium=social&utm_campaign=organic</a>

Guillaume GaullierI suspect <a href="https://fediscience.org/@waldo" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@waldo</a> is secretly trying to reprocess every <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> dataset available on EMPIAR. 🤔

Guillaume GaullierContinuing this thread of important <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> papers. ❄️ 🔬 📰 🧵I finally read: Henderson R (1995) The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Quarterly Reviews of Biophysics 28: 171–193 <a href="https://doi.org/10.1017/S003358350000305X" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1017/S003358350000305X</a>Some key points from this review:- Neutrons would be ideal if we had much brighter sources, lenses, and better detectors. 30 years after this review, sources have become brighter but still far from enough. Even if all of this was solved, it would be beneficial to use 15N labeled, per-deuterated biological macromolecules. NMR spectroscopists do this, but it is difficult and costly. All of this makes neutron microscopy very impractical. - The next best option is electrons, because they have the most favorable ratio of radiation damage per elastic scattering. - 30 years after the review, most of what was written about electron microscopy presenting the best opportunity for rapid improvement has indeed happened. See the growth of cryoEM as a structure determination method, and the 2017 Nobel Prize in chemistry. - The review has interesting calculations about the number of particles of a certain molecular weight necessary to achieve interpretable 3D reconstructions, assuming perfect images. Today's average cryoEM structure often achieves this with smaller or fewer particles (or even both smaller and fewer).

SBGridMeharry Medical College Ph.D. candidate KeAndreya Morrison's highlight features a PNAS publication from the laboratory of Paul Riegelhaupt of Weill Cornell Medicine that reveals how anesthetics shut down brain activity by closing the THIK1 potassium channel, offering new insight into how anesthesia works at the molecular level.Read more here: <a href="https://medium.com/sbgrid-community-news/unlocking-the-secrets-of-anesthesia-a-closer-look-at-the-thik1-k2p-channel-622d5cb89a27" target="_blank" rel="nofollow noopener noreferrer" translate="no">https://medium.com/sbgrid-community-news/unlocking-the-secrets-of-anesthesia-a-closer-look-at-the-thik1-k2p-channel-622d5cb89a27</a><a href="https://mstdn.science/tags/SBGrid" class="mention hashtag" rel="tag">#SBGrid</a> <a href="https://mstdn.science/tags/CryoEM" class="mention hashtag" rel="tag">#CryoEM</a> <a href="https://mstdn.science/tags/StructuralBiology" class="mention hashtag" rel="tag">#StructuralBiology</a>

Guillaume GaullierI'm going to keep appending to this thread when I catch up with reading important <a href="https://fediscience.org/tags/cryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cryoEM</a> papers. ❄️ 🔬 📰 🧵I recently read: Marques MA, Purdy MD & Yeager M (2019) CryoEM maps are full of potential. Current Opinion in Structural Biology 58: 214–223 <a href="https://doi.org/10.1016/j.sbi.2019.04.006" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1016/j.sbi.2019.04.006</a>It's a good review, full of pointers to important papers. Some of these were already on my radar, others not. I have a few I need to read now.Important bits from this review:- Asp and Glu side chains are often not detectable in cryoEM maps, for two reasons: carboxylate groups are more sensitive to radiation damage than other groups, and negatively charged oxygen has negative scattering factors at low resolution ranges. - We can learn a lot more from cryoEM maps than only atom coordinates, for example charges. - Because all charges scatter electrons, peak centroids in cryoEM maps (= Coulomb potential maps) don't perfectly coincide with atom centers, making atomic model refinement a bit trickier. Coulomb potential maps can be converted to charge density maps, making the peak centroids coincide with atom centers. One of the references cited explains how to do this conversion. I need to try this on a good map.

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