Operation of all CIISB Core facilities continues, for external users exclusively in a remote access mode. On-site visits of external users are temporarily banned. Please, contact the staff for details.
CIISB offers priority access to groups that need to use CIISB structural biology services for projects directly related to studies of the virus and projects aiming to develop an effective vaccine or treatment. To request priority access, please submit a research proposal with „COVID-19“ in the title of the proposal, through the online application system HERE. Successfully accepted proposals will be free of charge, and no financial contribution will be requested for the measurement/service.
Czech National Centre of the European Research Infrastructure Consortium INSTRUCT ERIC
A gateway to realm of structural data for biochemists, biophysicists, molecular biologist, and all scientists whose research benefits from accurate structure determination of biological macromolecules, assemblies, and complex molecular machineries at atomic resolution.
Open access to 10 high-end core facilities and assisted expertise in NMR, X-ray crystallography and crystallization, cryo-electron microscopy and tomography, biophysical characterization of biomolecular interaction, nanobiotechnology, proteomics and structural mass spectrometry.
A distributed infrastructure constituted by Core Facilities of CEITEC (Central European Institute of Technology), located in Brno, and BIOCEV (Biotechnology and Biomedicine Centre), located in Vestec near Prague, Central Bohemia.
CIISB offers priority and free-of-charge access for COVID-19 research proposals
CIISB is committed to the use its resources in response to the emergency situation of the COVID-19 virus pandemic. CIISB ensures that available technologies support primarily researchers in their efforts to study the virus and projects aiming to the development of an effective vaccine or treatment.
New EMBO Core Facility Fellowships
EMBO recently launched Core Facility Fellowships, which will support international training exchanges for staff working in core facilities that provide services to research institutes and universities.
Instruct-ERIC priority access for research proposals relating the SARS-CoV-2 virus
Instruct-ERIC is offering priority access to groups that need to use its structural biology services for projects directly related to COVID-19 viral proteins. Priority access will ensure a faster review of research proposals relating to COVID-19.
Postponed: Advanced methods in macromolecular crystallization IX
The main aim of this course is consideration of theoretical aspects of crystal growth process as well as practical work: there will be a healthy mix of advanced discussions of the theory and of laboratory experiments and the possibility for participants to crystallize their own proteins.
POSTPONED: Spring Workshop on BioAFM Microscopy
This event is going to bring together not only AFM researchers from bio field, but also other bio researchers and provide them an environment for fruitful networking and new possibilities in collaborations as well as enhance their knowledge in their field of research.
Cancelled: NMR Valtice 2020
Due to the COVID-19 pandemic situation in Europe, the 35th NMR Valtice meeting has been cancelled.
NMR in Valtice is the annual meeting of the nuclear magnetic resonance community and serves as the principal international forum for reporting outstanding research and development on new NMR methods, techniques and tools for research and application in science and technology.
the best of science obtained using CIISB Core Facilities
J. Am. Chem. Soc. 2020
Crystal structures of (A) PBD anthramycin covalently bound to DNA strands and (B) lincomycin targeting the peptidyl transferase center in the 50S ribosomal subunit of Staphylococcus aureus.
Antitumor pyrrolobenzodiazepines (PBDs), lincosamide antibiotics, quorumsensing molecule hormaomycin, and antimicrobial griselimycin are structurally and functionally diverse groups of actinobacterial metabolites. The common feature of these compounds is the incorporation of L -tyrosine- or L -leucine-derived 4-alkyl-L -proline derivatives (APDs) in their structures. In this study, the authors report that the last reaction in the biosynthetic pathway of APDs, catalyzed by F420 H2 -dependent Apd6 reductases, contributes to the structural diversity of APD precursors. Specifically, the heterologous overproduction of six Apd6 enzymes demonstrated that Apd6 from the biosynthesis of PBDs and hormaomycin can reduce only an endocyclic imine double bond, whereas Apd6 LmbY and partially GriH from the biosynthesis of lincomycin and griselimycin, respectively, also reduce the more inert exocyclic double bond of the same 4- substituted Δ 1-pyrroline-2-carboxylic acid substrate, making LmbY and GriH unusual, if not unique, among reductases. Furthermore, the differences in the reaction specificity of the Apd6 reductases determine the formation of the fully saturated APD moiety of lincomycin versus the unsaturated APD moiety of PBDs, providing molecules with optimal shapes to bind their distinct biological targets. Moreover, the Apd6 reductases establish the first F420 H2-dependent enzymes from the luciferase-like hydride transferase protein superfamily in the biosynthesis of bioactive molecules. Finally, bioinformatics analysis demonstrates that Apd6 and their homologues, widely distributed within several bacterial phyla, play a role in the formation of novel yet unknown natural products with incorporated L-proline-like precursors and likely in the microbial central metabolism.
Steiningerova, L. Kamenik, Z.*, Gazak, R., Kadlcik, S., Bashiri, G., Man, P., Kuzma, M., Pavlikova, M., and Janata, J.: Different Reaction Specificities of F420H2‑Dependent Reductases Facilitate Pyrrolobenzodiazepines and Lincomycin To Fit Their Biological Targets, J. Am. Chem. Soc. 2020, 142, 3440-3448, https://dx.doi.org/10.1021/jacs.9b11234
Nature Communications 2020
Cryo-EM structure of pT=4 quasi-icosahedral BDP and its penatameric and hexameric components. a Surface model of pT = 4 quasi-icosahedral BDP particle, displayed on the left side. A ribbon model of a cmcD pentamer and three cmcC′ hexamers is displayed on the right side. Pentameric cmcD protein is colored in yellow and hexameric cmcC′ is colored in green. Note that the fivefold symmetry axis is located at the center of cmcD pentamer and threefold axis is located in the middle between three cmcC′ hexamers. b Electrostatic surface potential of pentameric cmcD and hexameric cmcC′. Note the pores in the centers of pentamers and hexamers.
Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.
Kalnins, G., Cesle, E-E., Jansons, J., Liepins, J., Filimonenko, A., and Tars, K.: Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles, Nature Comm. (2020) 11 (1), No. 388, doi.org/10.1038/s41467-019-14205-y
literature to read, science to follow
In this section, a distinct selection of six highly stimulating research publications and reviews published during past 6 months is presented. It is our hope that links to exciting science, which deserves attention of the structural biology community, will help you to locate gems in the steadily expanding jungle of scientific literature. You are welcome to point out to any paper you found interesting by sending a link or citation to email@example.com. The section is being updated regularly.
Cryo-electron microscopy for the study of virus assembly
Although viruses are extremely diverse in shape and size, evolution has led to a limited number of viral classes or lineages, which is probably linked to the assembly constraints of a viable capsid. Viral assembly mechanisms are restricted to two general pathways, (i) co-assembly of capsid proteins and single-stranded nucleic acids and (ii) a sequential mechanism in which scaffolding-mediated capsid precursor assembly is followed by genome packaging. Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), which are revolutionizing structural biology, are central to determining the high-resolution structures of many viral assemblies as well as those of assembly intermediates. This wealth of cryo-EM data has also led to the development and redesign of virus-based platforms for biomedical and biotechnological applications. In this Review, recent viral assembly analyses by cryo-EM and cryo-ET are discussed, showing how natural assembly mechanisms are used to encapsulate heterologous cargos including chemicals, enzymes, and/or nucleic acids for a variety of nanotechnological applications.
The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy
Liquid-liquid phase separation (LLPS) of proteins and nucleic acids is a phenomenon that underlies membrane-less compartmentalization of the cell. The underlying molecular interactions that underpin biomolecular LLPS have been of increased interest due to the importance of membrane-less organelles in facilitating various biological processes and the disease association of several of the proteins that mediate LLPS. Proteins that are able to undergo LLPS often contain intrinsically disordered regions and remain dynamic in solution. Solution-state NMR spectroscopy has emerged as a leading structural technique to characterize protein LLPS due to the variety and specificity of information that can be obtained about intrinsically disordered sequences. This review discusses practical aspects of studying LLPS by NMR, summarizes recent work on the molecular aspects of LLPS of various protein systems, and discusses future opportunities for characterizing the molecular details of LLPS to modulate phase separation.
Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems
A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, Marco Sprangers and Stefan Schütz discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.
Integrative Structural Biology of Protein-RNA Complexes
Ribonucleoprotein complexes (RNPs) are central to all processes in the cell. One of the prerequisites to understand how RNPs work is to determine their high-resolution structures. With the recent revolution in cryo-electron microscopy this task has become easier for large RNP machines, such as ribosomes, spliceosomes, and polymerases. However, the transient and highly dynamic nature of many RNPs makes structure determination a challenging task. Thus, an integrative structural and molecular biology approach is required, tackling three key challenges: (1) identification of cognate RNA sequences; (2) collection of structural data by conducting X-ray crystallography, NMR, electron microscopy, small-angle scattering (SAS), and other experiments; and (3) the creation of structural models that integrates all experimental restraints. Given the breadth of expertise required, Janosch Henning et. al. in Structure present an overview of available methods and successful examples with the goal to provide readers with a selection of promising options for structure determination of RNPs.
Structural biology of cell surface receptor-ligand interactions
Plants have evolved unique membrane receptors that interpret native and foreign cues to coordinate plant life and adaptation. This large family of receptor proteins have evolved very diverse ectodomains, acquiring the capacity to sense ligands of very different chemical nature. A mechanistic understanding on how these signaling systems work will help to comprehend and unveil key cell biology questions. The review by Steven Moussou and Julia Santiago in Current Opinion in Plant Biology aims to focus on the latest receptor-ligands interactions and regulatory mechanism that have been structurally characterized, as well as new receptor folds.
Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats
Following the discovery of numerous long non-coding RNA (lncRNA) transcripts in the human genome, their important roles in biology and human disease are emerging. Recent progress in experimental methods has enabled the identification of structural features of lncRNAs. However, determining high-resolution structures is challenging as lncRNAs are expected to be dynamic and adopt multiple conformations, which may be modulated by interaction with protein binding partners. The X-inactive specific transcript (Xist) is necessary for X inactivation during dosage compensation in female placental mammals and one of the best-studied lncRNAs. Recent progress has provided new insights into the domain organization, molecular features, and RNA binding proteins that interact with distinct regions of Xist. The A-repeats located at the 5' end of the transcript are of particular interest as they are essential for mediating silencing of the inactive X chromosome. In this review, recent progress with elucidating structural features of the Xist lncRNA, focusing on the A-repeats is discussed. The experimental and computational approaches employed that have led to distinct structural models, likely reflecting the intrinsic dynamics of this RNA are overviewed. The presence of multiple dynamic conformations may also play an important role in the formation of the associated RNPs, thus influencing the molecular mechanism underlying the biological function of the Xist A-repeats. Alisha Jones and Michael Sattler in Journal of Molecular Cell Biology propose that integrative approaches that combine biochemical experiments and high-resolution structural biology in vitro with chemical probing and functional studies in vivo are required to unravel the molecular mechanisms of lncRNAs.
Quote of March
“The mediocre teacher tells. The good teacher explains. The superior teacher demonstrates. The great teacher inspires.”William Arthur Ward