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Editorial
It is with great pleasure that we congratulate Pavel Plevka on becoming the Director of CEITEC Masaryk University! Pavel, who took on this role in July 2024, will continue working as a member of the CIISB Executive Committee. Due to the additional workload associated with his new position, his duties as CIISB Chair will be taken over by Jiří Nováček. Jiří, based at CEITEC Masaryk University, serves as the Deputy Director for Research Infrastructure and heads the Cryo-electron Microscopy and Tomography Core Facility. In addition to his new role as Chair, Jiří will also represent CIISB in Instruct-ERIC as a member of the Instruct Executive Committee and Instruct Council.
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We are glad to share that Pavel will remain an active member of the CIISB Executive Committee, and mandates of all Executive Committee members have been extended for another two years, lasting until August 2026.
Additionally, we warmly welcome our new Scientific Advisory Board (SAB) members, Maria Marta Garcia Alai from EMBL Hamburg and Frank Sobott from the University of Leeds. They will join current SAB members Tomáš Obšil, Michael Sattler, and Jürgen Plitzko for the next five-year term, enhancing the strength of our advisory team. The constituent meeting of the SAB, alongside Executive Committee members and Heads of CIISB Core Facilities, is scheduled for November 14 in conjunction with the Vladimír Sklenář Memorial Conference. We invite you all to join us for this significant event to celebrate Professor Vladimír Sklenář, CIISB father-founder!
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Applications 2024
- 118 internal applications
- 76 external applications (Czech)
- 43 applications from foreign users
You can find more information here.
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2016 |
2017 |
2018 |
2019 |
2020 |
2021 |
2022 |
2023 |
2024 |
| Internal users |
123 |
178 |
177 |
147 |
183 |
166 |
129 |
135 |
118 |
| External users |
35 |
50 |
51 |
58 |
94 |
69 |
79 |
88 |
76 |
| Foreign users |
5 |
14 |
15 |
27 |
13 |
16 |
27 |
40 |
43 |
| Total |
163 |
242 |
243 |
232 |
289 |
251 |
235 |
263 |
237 |
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We are inviting you to a Practical Protein Crystallization and Diffraction Course held in the Centre of Molecular Structure on October 9-10, 2024.
For details and information on how to apply, please see the invitation.
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Curious about what expert services are available to researchers on campus? What instruments can you use in shared mode and under what conditions? Do you want to see everything for yourself?
Feel free to register for the Core Facility Day Life Sciences, which involves CEITEC, the Faculty of Science, the Faculty of Medicine, the Faculty of Pharmacy, the Faculty of Sport Studies, and the Institute of Computer Science.
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A two-day conference is organized in memory of our esteemed colleague and one of the most prominent and internationally recognized experts in the field of NMR and structural biology, Professor Vladimír Sklenář, who passed away on 13 April 2024. At the Central European Institute of Technology (CEITEC), Masaryk University, he was instrumental in establishing world-class research infrastructures in structural biology, particularly in NMR spectroscopy and electron microscopy. CIISB has established itself at the level of comparable workplaces in Western Europe thanks to his interactions with the Instruct-ERIC, European ESFRI infrastructure, where he acted as a member of the Executive Committee and Council. His tenure at the Faculty of Science of Masaryk University, CIISB and CEITEC was characterized by a great passion for scientific challenges and a great deal of humanity with which he approached his colleagues.
Lectures and contributions by invited speakers will bring back memories of Vladimir’s tenure and will present the latest scientific findings in structural biology and in NMR.
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We're excited to invite you to join us at the CTLS 2025 Congress happening in the beautiful city of Brno from 10-12 June 2025! This gathering is going to be an excellent opportunity, bringing together core facility administrators, managers, researchers, and professionals to talk, collaborate, and dive into why core facilities are key to shaping the scientific world. Don't miss out and check the congress website, where all the information are being published!
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Meet Pavel Kadeřávek, new Head of CF NMR
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Pavel Kadeřávek became the new head of the Josef Dadok National NMR Centre on 1 July 2024. Pavel has a scientific background in NMR methodology development, study of biomolecule dynamics, characterization of minority states of biomolecules and IDPs.
Why did you choose to be in the position of CF Head? Because I consider working in the NMR core facility to be a valuable service to other scientists, to which I feel a certain sense of vocation. At the same time, I expect that this position will enhance my understanding of the technical aspects of NMR operations and expand my knowledge of the practical functioning of the NMR core facility from a new perspective.
What excites you the most about your job? I am most attracted by the possibilities for further methodological development of NMR, in which I can also participate from my position. This method already contains a huge number of designed experiments that can be used for different purposes, which in itself allows for a lifetime of learning in this field. In addition, I believe that it has not yet revealed all its potential and applications.
What are the obstacles you need to overcome? The biggest challenge we face is the unfavorable economic outlook for the operation of the NMR facility. Recently, the prices of liquid helium have risen significantly, which, along with the substantial increase in repair costs, excessively raises our operating expenses. Additionally, the European project iNEXT-Discovery, which funded access to measurements for external users (not only at our facility) and was a significant source of our financial stability, has recently ended.
How do you relax and clear your head? My relaxation is hiking in places that are not overcrowded.
Radovan Fiala, who has led the facility since its establishment in 2012, remains deputy head to ensure a smooth CF handover and plans to reduce his working time before he goes to a well-deserved retirement. Radovan's role in the functioning of the CF, which reaches European standards, has always been a model for all other CFs that have been established at CEITEC over time.
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CIISB Research Highlights
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Nucleic Acid Research 2024
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DNA binding to CggR in the cryo-EM structure. Model of the CggR–OLR biological unit fitted to a cryo-EM map.
Pavlina Rezacova Research Group
Significance:
The SorC family of transcriptional regulators plays a crucial role in controlling the carbohydrate metabolism and quorum sensing. We employed an integrative approach combining X-ray crystallography and cryo-electron microscopy to investigate architecture and functional mechanism of two prototypical representatives of two sub-classes of the SorC family: DeoR and CggR from Bacillus subtilis. Despite possessing distinct DNA-binding domains, both proteins form similar tetrameric assemblies when bound to their respective DNA operators. Structural analysis elucidates the process by which the CggR-regulated gapA operon is derepressed through the action of two effectors: fructose-1,6-bisphosphate and newly confirmed dihydroxyacetone phosphate. Our findings provide the first comprehensive understanding of the DNA binding mechanism of the SorC-family proteins, shedding new light on their functional characteristics.
Soltysova M. et al. Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function
Nucleic Acid Research 2024, 52(12), 7305-20, DOI: 10.1093/nar/gkae434
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Nature Communications 2024-2
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Structural details of the highlighted MsmIMPDH monomer.
Tomáš Kouba Research Group
Significance
Allosteric regulation of inosine 5′-monophosphate dehydrogenase (IMPDH), an essential enzyme of purine metabolism, contributes to the homeostasis of adenine and guanine nucleotides. However, the precise molecular mechanism of IMPDH regulation in bacteria remains unclear. Using biochemical and cryo-EM approaches, we reveal the intricate molecular mechanism of the IMPDH allosteric regulation in mycobacteria. The enzyme is inhibited by both GTP and (p)ppGpp, which bind to the regulatory CBS domains and, via interactions with basic residues in hinge regions, lock the catalytic core domains in a compressed conformation. This results in occlusion of inosine monophosphate (IMP) substrate binding to the active site and, ultimately, inhibition of the enzyme. The GTP and (p)ppGpp allosteric effectors bind to their dedicated sites but stabilize the compressed octamer by a common mechanism. Inhibition is relieved by the competitive displacement of GTP or (p)ppGpp by ATP allowing IMP-induced enzyme expansion. The structural knowledge and mechanistic understanding presented here open up new possibilities for the development of allosteric inhibitors with antibacterial potential.
Bulvas, O., Knejzlík, Z., Sýs, J. et al. Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase.
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Angewandte Chemie Int. Ed. 2024-2
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Structure-transformation analysis: reversible conversion reaction between Pd3(L1)6 and trimeric Pd3(L1)3Cl6 species suggesting the existence of a crown-like architecture.
Radek Marek and Ondrej Jurcek Research groups
Significance:
Nature uses various chiral and unsymmetric building blocks to form substantial and complex supramolecular assemblies. In contrast, the majority of organic ligands used in metallosupramolecular chemistry are symmetric and achiral. Here we extend the group of unsymmetric chiral bile acids used as a scaffold for organic bispyridyl ligands by employing chenodeoxycholic acid (CDCA), an epimer of the previously used ursodeoxycholic acid (UDCA). The epimerism, flexibility, and bulkiness of the ligands leads to large structural differences in coordination products upon reaction with Pd(NO3)2. The UDCA-bispyridyl ligand self-assembles quantitatively into a single crown-like Pd3L6 complex, whereas the CDCA ligand provides a mixture of coordination complexes of general formula PdnL2n, i.e., Pd2L4, Pd3L6, Pd4L8, Pd5L10, and even Pd6L12 containing an impressive 120 chiral centers. The coordination products were studied by a combination of analytical methods, with ion-mobility mass spectrometry (IM-MS) providing valuable details on their structure and allowed an effective separation of m/z 1461 to individual signals according to the arrival time distribution, thereby revealing four different ions of [Pd3L6(NO3)3]3+, [Pd4L8(NO3)4]4+, [Pd5L10(NO3)5]5+, and [Pd6L12(NO3)6]6+. The structures of all the complexes were modelled using DFT calculations. Finally, the challenges and conclusions in determining the specific structural identity of these unsymmetric species are discussed.
Jurcek O. et al. Unsymmetric Chiral Ligands for Large Metallo-Macrocycles: Selectivity of Orientational Self-Sorting
Angewandte Chemie International Edition 2024, 63(36), e202409134, DOI: 10.1002/anie.202409134
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Cryo-EM micrographs of the JBD30 virions binding to Type IV pili.
Pavel Plevka Research Group
Significance:
Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosavia the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment.
Valentova L. et al. Structure and replication of Pseudomonas aeruginosa phage JBD30
EMBO Journal 2024, DOI: 10.1038/s44318-024-00195-1
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The Protein production facility in Biocev has realized the first eukaryotic expression project
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The Protein production facility at IBT-Biocev has provided services of cloning, bacterial protein expression and protein purification for several years. In a response to users' demand an extension of the services to eukaryotic expression has been planned and realized. We would like to thank the support from IBT and Biocev in securing suitable laboratory space for this extension. Recently, the Protein production facility has performed the first eukaryotic expression project(s) and expects its full operation in this area in 2025.
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Installation Falcon4i direct electron detector with Selectris energy filter at CEITEC Masaryk University
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The Cryo-electron Microscopy and Tomography Core Facility at CEITEC Masaryk University has successfully finished the installation of the state-of-the-art Falcon4i direct electron detector combined with the Selectris energy filter on the Talos Arctica transmission electron microscope. This advanced system is now available to all users of the CIISB cryo-EM facility, offering enhanced capabilities for both single particle analysis and cryo-electron tomography. The installation will increase the throughput and data quality, facilitating higher quality data and more efficient data collection. The system’s performance was rigorously tested using an apoferritin sample, achieving a resolution of <2Å from data collected within just a few hours of data acquisition time. The installation of Selectris-Falcon4i was made possible through the "Innovation of Czech Infrastructure for Integrative Structural Biology" grant, funded by the OP JAK for Research Infrastructures I.
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Renishaw's InVia confocal Raman microscope - update
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Raman microscopy is a technique that combines spectroscopy with optical microscopy to determine the chemical composition of a sample with micrometer resolution. The Raman signal originates from the vibrations of chemical bonds and has an absolute value. We talk about the so-called fingerprint method. Renishaw's InVia confocal Raman microscope has been used in the central nanobiotechnology laboratory since 2020. Its use was often limited by a 633 nm universal laser, which caused autofluorescence, particularly in biological samples.
As part of an upgrade funded by the Innovation of Czech Infrastructure for Integrative Structural Biology grant (reg. no. CZ.02.01.01/00/23_015/0008175.) funded by the OPJAK for Research Infrastructures I, a 785-nm diode laser was added to the system to address this shortcoming. In addition, the CCD camera module and the optical part of the microscope were upgraded to allow imaging in darkfield and oil and water immersion. The new version of the software allows the creation of user-defined databases and automatic part analysis, which users will appreciate especially for the recently requested analysis of microplastics and other materials containing microparticles, such as pharmaceutical substances.
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O. Sedo, et al.: Discriminatory power of MALDI-TOF MS protein profiling analysis of pork meat and meat products, Food Chemistry, 449 (2024) 11, 10.1016/j.foodchem.2024.139155
L. Valentová, et al.: Structure and replication of Pseudomonas aeruginosa phage JBD30, Embo J., (2024) 22, 10.1038/s44318-024-00195-1
O. Jurcek, et al.: Unsymmetric Chiral Ligands for Large Metallo-Macrocycles: Selectivity of Orientational Self-Sorting, Angewandte Chemie-International Edition, 63 (2024) 8, 10.1002/anie.202409134
H.G. Changela, et al.: The evolution of organic material on Asteroid 162173 Ryugu and its delivery to Earth, Nature Communications, 15 (2024) 14, 10.1038/s41467-024-50004-w
B. Manori, et al.: Chloride intracellular channel (CLIC) proteins function as fusogens, Nature Communications, 15 (2024) 14, 10.1038/s41467-024-46301-z
M. Soltysová, et al.: Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function, Nucleic Acids Res., 52 (2024) 7305-7320, 10.1093/nar/gkae434
D. Jankovská, et al.: Anticholinesterase Activity of Methanolic Extract of Amorpha fruticosa Flowers and Isolation of Rotenoids and Putrescine and Spermidine Derivatives, Plants-Basel, 13 (2024) 10, 10.3390/plants13091181
M. Anastasina, et al.: The structure of immature tick-borne encephalitis virus supports the collapse model of flavivirus maturation, Sci. Adv., 10 (2024) 13, 10.1126/sciadv.adl1888
P. Lapcik, et al.: A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer, Sci. Data, 11 (2024) 7, 10.1038/s41597-024-03632-2
J. Sistkova, et al.: Insight into antibacterial effect of titanium nanotubular surfaces with focus on Staphylococcus aureus and Pseudomonas aeruginosa, Sci Rep, 14 (2024) 20, 10.1038/s41598-024-68266-1
F. Niro, et al.: Fibrotic extracellular matrix impacts cardiomyocyte phenotype and function in an iPSC-derived isogenic model of cardiac fibrosis, Transl. Res., 273 (2024) 58-77, 10.1016/j.trsl.2024.07.003
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