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Editorial
Dear Colleagues,
the conclusion of summer offers a chance to reflect on the CIISB accomplishments achieved in 2023.
A crucial task for 2023 was the preparation of an application to OP JAK Call 02_23_015 Research Infrastructures I, which will provide support for reinvesting in the current equipment and purchasing new instrumentation for the years 2024–2026. With a carefully selected range of instruments for upgrading and purchasing, CIISB will strive to maintain its competitiveness on the European level and reinforce its position as one of the leading Instruct Centers,
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providing international access to its flagship technologies within the Instruct-ERIC European Infrastructure collaboration. The project was successfully submitted on 21st August 2023, with a request to invest nearly 300 million CZK between 2024 and 2026. I would like to thank all my colleagues who participated in the preparation of the project and supported it with their invaluable contributions. The results are expected to be published by the end of 2023.
Despite the budget cuts affecting project LM2023042, which sustains the running costs of the CIISB core facilities, the operations and access provisions have been maintained at the expected level. A review of the publications supported by CIISB at the Web of Science since January 2023 counts 59 papers, including articles in distinguished journals like Nature, Nature Plants, Nature Structural and Molecular Biology, Nature Communications, Small, Journal of the American Chemical Society, and Nucleic Acids Research.
On 23-25 March 2023, the annual Czech Structural Biology Society meeting and the CIISB users' meeting were held in Nové Hrady. The 19th Discussions in Structural Molecular Biology and the 6th User Meeting of CIISB were well-attended events where the scientific program included 27 presentations, 7 quick presentations, and 46 posters. A total of 135 participants enjoyed the events. Our congratulations go to the winners of the Student Competition, namely Michaela Novotná, Zuzana Trebichalská, and Július Zemaník for their poster presentations, and Lucie Valentová, Karolína Honzejková, and Ondřej Bulvas for their oral contributions.
Other meetings organized or co-organized by CIISB, and worth mentioning, included Core Facility Nanobiotechnology: Where we are and where to go next…, March 7, 2023; iNEXT-D hands-on workshop on cryo-FIB lamella preparation & cryo electron tomography, April 17-21,2023; ESC5: Label-free techniques for the characterization of protein interactions, May 3-5, 2023; SPACET 2023, May 17-21, 2023; Instruct-ERIC Best Practices in Cryo-EM Workshop, May 23-24, 2023; and 3rd CEITEC Symposium on Recent Advances in Cryo-EM, May 25-26, 2023. Information about the upcoming events and the latest news from CIISB, including Research CIISB Highlights and Readers Corner paper selections, are available on our web www.ciisb.org.
I wish you an enjoyable and successful rest of the year 2023.
August 31, 2023
Pavel Plevka
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The Bertini Award 2024 call is open, submit your nominations for the winner before the deadline of 30 September 2023.
The winner will be announced at the Biennial Structural Biology Conference, in May 2024.
Nominations are invited for the Award for a significant achievement in any area of integrated structural biology. Self-nominations are not accepted.
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Welcome to the 23rd Central European Users Meeting (13-15 September 2023, Faculty of Architecture - Prague, Czech Republic), a scientific event dedicated to NMR users and enthusiasts. This year's event promises to be engaging, informative, and productive, with a range of presentations, discussions, and networking opportunities.
The agenda for the event is now available on the website, where you can also find all the information you need to attend, including the registration form. Take a look!
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The Instruct-ERIC Biennial Structural Biology Conference 2024 (IBSBC2024) will be taking place 22-24 May 2024.
The conference showcases the latest in integrative structural biology from leading scientists across the world, and will be taking place in the sunny seaside town of Cascais, Portugal.
This is the 6th Biennial Conference, and will explore the latest cutting-edge developments in structural biology, including imaging technologies, artificial intelligence and more, as well as insight into the role structural biology plays in the wider global context.
Biennial registration is open now.
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Registration is open to join the first IMAGINE meeting open to all Instruct Centres on the 15th of September 2023 from 14:00 to 17:00 CEST. This meeting will highlight the new services (imaging instrumentation, tools and methods...) developed in the project and initiate collaborations with Instruct Centres external to IMAGINE. Indeed, Instruct Centres external to IMAGINE might take part in the validation and testing of the new services developed.
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eBIC, Diamond Light Source, are pleased to announce the iNext-Discovery Sample Preparation Course 2023. Thiscourse is aimed at newcomers to the field of single particle analysis (SPA) using cryo-EM for their research.
The course will run at Diamond, Oxfordshire, UK on 16-19 Oct 2023. Delegates can expect theoretical lectures from expert & active scientists in the field including, Becky Thompson (TFS), Pete Harrison (eBIC) and Miriam Weckener (SPT Labtech), vitrification demonstration and hands on time using vitrobots or GP2, screening and data collection practical(s) on a Titan Krios, as well as demonstration of next generation freezing technologies i.e. SPT Labtech Chameleon.
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We are inviting you to MOBSRI's End User Short Coursewhich will be held in Rome in October.
The course will be focused on the application of advanced kinetics techniques (stopped flow binding and folding experiments, FRET, T-Jump) to study protein structure and functions and to dissect several kinetics mechanisms.
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Congratulations to the latest R&D Pilot Project Call Awardees Alexandre Ourjoumtsev, IBMC, France, Steffen Klein, EMBL Heidelberg, Germany, Francesca Paoletti, University of Trieste, Italy, and Heikki Saari, Finnish Red Cross Blood Service, Finland. All have received funding for preliminary research through Instruct-ERIC. The call was for small scale research projects in integrated structural biology, helping researchers develop external funding for projects. The selected researchers will each receive 15 000 EUR and will utilise several key technologies in the Instruct-ERIC service catalogue. R&D Projects will take place over the next 12 months and will pave the way for innovative advances in integrated structural biology.
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Greece and Slovenia have joined the Instruct-ERIC Consortium, taking the total number of Member Countries and Organisations to 16.
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A new scanning electron microscope (SEM) equipped with the focused ion beam (FIB) operating on the principle of inductively-coupled plasma is available for service at CEITEC Masaryk University.
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We are pleased to announce a 5-day iNEXT-Discovery In-cell NMR Training Course, which will be held on 25th-29th September 2023 at CERM/CIRMMP in Florence, Italy.
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As announced previously, wwPDB, in collaboration with the PDBx/mmCIF Working Group, has set plans to extend the length of accession codes (IDs) for PDB and Chemical Component Dictionary (CCD) entries in the future.
PDB entries containing these extended IDs will not be supported by the legacy PDB file format.
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Applications 2023
- 99 internal applications
- 52 external applications (Czech)
- 18 applications from foreign users
You can find more information here.
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| External users |
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| Foreign users |
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Two days practical course on the basics of biological Small Angle X-ray Scattering (SAXS) is organised on September 5-6th, 2023 located in Brno, CEITEC (Central European Institute of Technology).
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CF Nanobio CEITEC of Masaryk University invites you to participate in the BioAFM Microscopy 2023 summer workshop, which will take place from 6 to 8 September 2023.
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The workshop (from 7 to 8 September 2023) is focused on high-throughput interaction screening using the Isothermal Spectral Shift technology. Researchers from both the academia and industrial sector will find out how you can increase the efficiency of your research during technical seminars. During hands on session, participants can learn about the newest impact screening platform Dianthus using Isothermal Spectral Shift technology and they will have an opportunity to test their samples using Dianthus and PR Panta instruments. The workshop is organized in collaboration with NanoTemper Technologies.
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A one-day demo (22 September 2023) of a plate-based differential scanning fluorimeter SUPR-DSF (Protein Stable) with an opportunity to measure your own samples. All specific questions will be possible to directly discuss with the company specialist.
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A two-day workshop (from 12 to 13 October) focused on mass photometry. In advance, the participants can attend an online webinar (October 2nd) focused on the theoretical background, technical details and benefits of measuring the size of molecule and their complexes in low volume and concentrations. Practical part will follow the next week with an opportunity to measure their own samples on Refeyn Two mass photometry system. All specific questions will be possible to directly discuss with Refeyn specialists.
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The Instruct-ERIC Biennial Structural Biology Conference 2024 (IBSBC2024) will be taking place 22-24 May 2024.
The conference showcases the latest in integrative structural biology from leading scientists across the world, and will be taking place in the sunny seaside town of Cascais, Portugal.
This is the 6th Biennial Conference, and will explore the latest cutting-edge developments in structural biology, including imaging technologies, artificial intelligence and more, as well as insight into the role structural biology plays in the wider global context.
Biennial registration will open soon.
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CIISB Research Highlights
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Nature Communications 2023
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Cryo-EM density maps showing side views of ISG65:C3 (left), and ISG65:C3b (right) at two different angles. ISG65 is represented by map regions coloured in green. Interacting domains in C3 and C3b are depicted in blue. In both C3 conformations, TED provides the primary interface. ISG65 and TED show a high degree of shape complementarity. Smaller, secondary interfaces are located in ANA (native C3) and CUB (C3b). The remaining scaffold (C3c, grey) shows no additional contact points.
Sebastian Zoll Research Group
Significance
African Trypanosomes have developed elaborate mechanisms to escape the adaptive immune response, but little is known about complement evasion particularly at the early stage of infection. Here we show that ISG65 of the human-infective parasite Trypanosoma brucei gambiense is a receptor for human complement factor C3 and its activation fragments and that it takes over a role in selective inhibition of the alternative pathway C5 convertase and thus abrogation of the terminal pathway. No deposition of C4b, as part of the classical and lectin pathway convertases, was detected on trypanosomes. We present the cryo-electron microscopy (EM) structures of native C3 and C3b in complex with ISG65 which reveal a set of modes of complement interaction. Based on these findings, we propose a model for receptor-ligand interactions as they occur at the plasma membrane of blood-stage trypanosomes and may facilitate innate immune escape of the parasite.
Sülzen, H., Began, J., Dhillon, A. et al. Cryo-EM structures of Trypanosoma brucei gambiense ISG65 with human complement C3 and C3b and their roles in alternative pathway restriction.
Nat Commun 14, 2403 (2023). https://doi.org/10.1038/s41467-023-37988-7
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Overview of the dormant ribosome structure from 1 hpf zebrafish (a) and Xenopus egg (b). Ribosome-associated factors are shown as surface representations; eEF2b and eIF5a correspond to Protein Data Bank (PDB) accessions 6MTE and 5DAT, respectively.
Andrea Pauli Research Group
Significance
Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4–eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1 in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.
Leesch, F. et. al.: A molecular network of conserved factors keeps ribosomes dormant in the egg, Nature (2023), 613, 712-720: https://doi.org/10.1038/s41586-022-05623-y
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H. Sulzen, et al.: Cryo-EM structures of Trypanosoma brucei gambiense ISG65 with human complement C3 and C3b and their roles in alternative pathway restriction, Nature Communications, 14 (2023) 18, 10.1038/s41467-023-37988-7
M. Nemergut, et al.: Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer's Disease drug candidate, Molecular Neurodegeneration, 18 (2023) 25, 10.1186/s13024-023-00620-9
B. Hustakova, et al.: A highly active S1-P1 nuclease from the opportunistic pathogen Stenotrophomonas maltophilia cleaves c-di-GMP, Febs Letters, (2023) 16, 10.1002/1873-3468.14683
Z. Bytesnikova, et al.: New insight into the biocompatibility/toxicity of graphene oxides and their reduced forms on Chlamydomonas reinhardtii, NanoImpact, 31 (2023) 12, 10.1016/j.impact.2023.100468
K. Hanelova, et al.: Autophagy modulators influence the content of important signalling molecules in PS-positive extracellular vesicles, Cell Commun. Signal., 21 (2023) 21, 10.1186/s12964-023-01126-z
K. Mrazova, et al.: Urany-Less Low Voltage Transmission Electron Microscopy: A Powerful Tool for Ultrastructural Studying of Cyanobacterial Cells, Microorganisms, 11 (2023) 13, 10.3390/microorganisms11040888
L. Janacova, et al.: Catechol-O-methyl transferase suppresses cell invasion and interplays with MET signaling in estrogen dependent breast cancer, Sci Rep, 13 (2023) 14, 10.1038/s41598-023-28078-1
Z. Hasanova, et al.: Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor, Nucleic Acids Res., (2023) 20, 10.1093/nar/gkad092
J. Houser, et al.: The NFkB activation domain is 14-amino-acid-long variant of the 9aaTAD, Biochem. J., 480 (2023) 297-306, 10.1042/bcj20220605
T.O. Koller, et al.: The Myxobacterial Antibiotic Myxovalargin: Biosynthesis, Structural Revision, Total Synthesis, and Molecular Characterization of Ribosomal Inhibition, Journal of the American Chemical Society, (2023) 13, 10.1021/jacs.2c08816
S. Legartova, et al.: Irradiation potentiates p53 phosphorylation and p53 binding to the promoter and coding region of the TP53 gene, Biochimie, 204 (2023) 154-168, 10.1016/j.biochi.2022.09.013
A. Makarov, et al.: The role of invariant surface glycoprotein 75 in xenobiotic acquisition by African trypanosomes, Microb. Cell, 10 (2023) 18-35, 10.15698/mic2023.02.790
S. Tanasa, et al.: A complex role of Arabidopsis CDKD;3 in meiotic progression and cytokinesis, Plant Direct, 7 (2023) 16, 10.1002/pld3.477
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