www.ciisb.org  |  1 Mar 2023, 15:16



Dear colleagues,

The beginning of a new year presents time to review the most significant events for CIISB from the year 2022 and highlight the critical challenge for 2023.

CIISB continued to support publications in prestigious journals. 20 of the 95 publications that were published in 2022 were in journals that are listed in the Nature index, bringing the total amount since 2016 to 563. Research Highlights provides an overview of the most noteworthy findings. The section Publications written with the support of CIISB on the CIISB website contains the results of additional significant papers.

In December 2022, the financing for Major Research Infrastructures for the years 2020 to 2022 came to an end, along with the project LM2018127. Due to the government's wise decision, funding for large research infrastructures will remain in place from 2023 to 2026. Within the new project LM2023042, CIISB will get a budget that is reduced relative to our expectations. As a result of these cuts, user fee contribution will have to be slightly increased (for some core facilities already in 2023, but mainly in 2024). Nevertheless, all core facilities will remain fully operational. The new project number LM2023042 should be acknowledged in all papers released in the upcoming fiscal year.

A crucial task for 2023 is 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 justified selection of instruments to upgrade and purchase, CIISB will aim to maintain its competitiveness on the European level and strengthen its position as one of the top Instruct Centers offering global access to its flagship technologies within the Instruct-ERIC European Infrastructure collaboration.

I look forward to meeting many of you at the XIX Discussions in Structural Molecular Biology Society and 6th User Meeting of CIISB in Nové Hrady, March 23-25, 2023.

I wish you an enjoyable and successful year in 2023.

February 28, 2023

Pavel Plevka

CMS workshop on Nano Themer technologies

CMS with experts from NanoTemper company are organizing a workshop on the proteins stability and size determination by Prometheus Panta and biomolecular interaction characterization by Monolith NT.115. The workshop will take place on 4-5 October.

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Re-open calls for transnational access for projects focusing on Monkeypox research and SARS-CoV-2 research

ISIDORe just re-opened the calls for transnational access for projects focusing on Monkeypox research and SARS-CoV-2 research.

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Workshop on Single Cell Proteomics

We would like to invite you to join our first Workshop on Single Cell Proteomics, which will be held on Monday, 11th of November 2022 in BioCev.

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Training Course - NMR for combatting disease

Register now to the training course from ICGEB and CERM/CIRMMP on NMR for combatting diseases. the The course will take place from 27 March to 31 March 2023.

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ISIDORe Webinar and Calls

ISIDORe is hosting a webinar 29 November to outline the ongoing and upcoming calls opened by the project.
RG4 Pathogens
Respiratory pathogens (excluding SARS-CoV-2)
Vector-borne pathogens and their vectors
Other pathogens with epidemic potential (including Disease X)

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AlphaFold’s new rival? Meta AI predicts shape of 600 million proteins

Researchers at Meta (formerly Facebook, headquartered in Menlo Park, California) have used AI to predict the structures of some 600 million proteins from bacteria, viruses and other microorganisms that haven’t been characterized.

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ISIDORe Preparedness Programme Calls for Proposals are Open for Applications

We are happy to inform you that 4 new calls have just been launched in ISIDORe, opening access to Research Infrastructures including Instruct-ERIC for projects focusing on a selection of pathogens in these 4 categories:

  • Risk group 4 pathogens
  • Respiratory pathogens (excluding SARS-CoV-2)
  • Vector-borne pathogens & their vectors
  • Other pathogens with epidemic or pandemic potential
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Instruct-ERIC New Coordination Team

Instruct-ERIC Director Prof. Harald Schwalbe has appointed Dr Claudia Alen Amaro and Dr Natalie Haley as the new Hub Coordination Team.

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The Alpine Conference on Magnetic Resonance in Solids 2023

This is a first announcement for the Alpine “Chamonix” Conference on Magnetic Resonance in Solids, that will take place in Chamonix Mont-Blanc, France, on 10-14 September 2023.

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13th conference "NMR, a tool for Biology"

We are very pleased to announce that the 13th "NMR, a tool for Biology" conference will be held at the Institut Pasteur in Paris from May 15th to 17th, 2023.

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NMR Symposium and Workshop 2023, ISTA Campus

On May 2 and 3, 2023 the Nuclear Magnetic Resonance Symposium will take place at the Institute of Science and Technology Austria (ISTA). The days after, May 4 and 5, 2023, a NMR workshop will be held for a select group of PhD students.

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EMBO Workshop: Visualising the complex dynamics of biological membranes

The EMBO workshop "Visualising the complex dynamics of biological membranes” is on March 13-16, at the Tel Aviv University.


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Instruct-ERIC R&D Call Open

Instruct allocates funds to support small pilot research and development projects in any area of structural biology up to a maximum of €15,000 per project.

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Talk of Dr. Alcicek on Zero- and Ultralow-field NMR

We are pleased to announce that the third Kiel Imaging Seminar (KIS) will take place next Monday, January 16th.


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Prototype of PDB NextGen Archive now available

A prototype of a next generation archive repository for the PDB is now available.

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Spin Hyperpolarisation Symposium

Registration is now open for the Spin Hyperpolarisation Symposium, 27/28 April 2023, Nottingham University, UK.

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Congratulations to the Winner of the 2022 PhD Thesis Award Dominik Hrebík

The prize will be awarded for his outstanding PhD thesis entitled Characterization of viral cell entry in vivo and ex vivo, defended at the Faculty of Science, Masaryk University, Brno. We congratulate Dominik and his supervisor Pavel Plevka.

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CIISB Access

Applications 2022

  • 129 internal applications
  • 79 external applications (Czech)
  • 27 applications from foreign users

You can find more information here.

Application overview in total

  2016 2017 2018 2019 2020 2021 2022
Internal users 123 178 177 147 183 166 129
External users 35 50 51 58 94 69 79
Foreign users 5 14 15 27 13 16 27
Acces Overview

Save the date

The XIX Discussions in Structural Molecular Biology and the 6th User meeting of CIISB in Nové Hrady

Come and experience the unique atmosphere of the friendly small conference, present a talk or poster, possibly feature your poster in a flash talk, or just enjoy the science and company of your colleagues and learn the latest from the field in our country.

The XIX Discussions in Structural Molecular Biology and the 6th User Meeting of CIISB will be held in Nove Hrady, South Bohemia, on 23-25 March 2023

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36th NMR Valtice conference

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. Conference will be held April 2 – 5 2023.

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CIISB Research Highlights

Nature 2022

a, Kinome tree representation of the selectivity of OTS964 (at 1 µM concentration) in the Eurofins panel of 412 human kinases. The size of the red circles shows the percentage of inhibition of kinase activity. The green circle corresponds to CDK11. The percentage of CDK11 inhibition was derived from IVKAs presented in b and Fig. 3f The blue circle corresponds to TOPK. The percentage of TOPK inhibition was estimated from the published IC50 = 353 nM and Extended Data Fig. 1b. b, Immunoblots of IVKAs of Flag-tagged (F) CDK11 WT, G579S and kinase dead (KD) mutants (left), or Flag-tagged CDK9 WT and KD mutant (right) phosphorylation of glutathione-S-transferase (GST)-tagged RNAPIICTD substrate with the indicated concentrations of OTS964. c, The percentage of normalized NanoBRET ratio for CDK11/cyclin L2 or CDK9/cyclin T1 after OTS964 or control dinaciclib treatment. n = 2 biologically independent replicates; a representative replicate is shown. d, Immunoblot analysis of proteins after treatment of cells with OTS964 for 4 h. Short and long indicate short and long exposures of the film.

Dalibor Blažek Research Group


RNA splicing, the process of intron removal from pre-mRNA, is essential for the regulation of gene expression. It is controlled by the spliceosome, a megadalton RNA–protein complex that assembles de novo on each pre-mRNA intron through an ordered assembly of intermediate complexes. Spliceosome activation is a major control step that requires substantial protein and RNA rearrangements leading to a catalytically active complex. Splicing factor 3B subunit 1 (SF3B1) protein—a subunit of the U2 small nuclear ribonucleoprotein—is phosphorylated during spliceosome activation, but the kinase that is responsible has not been identified. Here we show that cyclin-dependent kinase 11 (CDK11) associates with SF3B1 and phosphorylates threonine residues at its N terminus during spliceosome activation. The phosphorylation is important for the association between SF3B1 and U5 and U6 snRNAs in the activated spliceosome, termed the Bact complex, and the phosphorylation can be blocked by OTS964, a potent and selective inhibitor of CDK11. Inhibition of CDK11 prevents spliceosomal transition from the precatalytic complex B to the activated complex Bact and leads to widespread intron retention and accumulation of non-functional spliceosomes on pre-mRNAs and chromatin. We demonstrate a central role of CDK11 in spliceosome assembly and splicing regulation and characterize OTS964 as a highly selective CDK11 inhibitor that suppresses spliceosome activation and splicing.

Hluchý, M., Gajdušková, P., Ruiz de los Mozos, I., Rájecký, M., Kluge, M., Berger, B-T., Slabá, Z., Potěšil, D., Weiß, E., Ule, J., Zdráhal, Z., Knapp, S., Paruch, K., Friedel, C.C., and Blažek, D.:

CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1, Nature. (2022) 609, 829-834. https://doi.org/10.1038/s41586-022-05204-z

Nature Communications 2022

a)Ribbon diagram of the NKR-P1 CTLD. Secondary structure elements are labeled in different colors: helix α1 is red, helix α2 is yellow, and β-strands and loops are cyan. b)Comparison between NKR-P1 dimers formed by the glycosylated (cyan), deglycosylated free (green), and LLT1-bound (blue) forms of NKR-P1. c) Comparison between helices α1- and α2-centered dimerization of murine dectin-1 (magenta) and human LLT1 (green), respectively; helices α1 and α2 are shown in red and yellow. Structural alignments of dectin-1 and NKR-P1 homodimers and LLT1 and NKR-P1 homodimers, prepared by aligning only one monomer from each dimer, are shown on the right-hand side. Although the CTLD fold is conserved in each pair of the aligned monomers, the helix α1- and helix α2-centered dimers show inverse arrangement.

Ondřej Vaněk Research Group


Signaling by the human C-type lectin-like receptor, natural killer (NK) cell inhibitory receptor NKR-P1, has a critical role in many immune-related diseases and cancer. C-type lectin-like receptors have weak affinities to their ligands; therefore, setting up a comprehensive model of NKR-P1-LLT1 interactions that considers the natural state of the receptor on the cell surface is necessary to understand its functions. Here we report the crystal structures of the NKR-P1 and NKR-P1:LLT1 complexes, which provides evidence that NKR-P1 forms homodimers in an unexpected arrangement to enable LLT1 binding in two modes, bridging two LLT1 molecules. These interaction clusters are suggestive of an inhibitory immune synapse. By observing the formation of these clusters in solution using SEC-SAXS analysis, by dSTORM super-resolution microscopy on the cell surface, and by following their role in receptor signaling with freshly isolated NK cells, we show that only the ligation of both LLT1 binding interfaces leads to effective NKR-P1 inhibitory signaling. In summary, our findings collectively support a model of NKR-P1:LLT1 clustering, which allows the interacting proteins to overcome weak ligand-receptor affinity and to trigger signal transduction upon cellular contact in the immune synapse.

Blaha, J., Skalova, T. Kalouskova, B., Skorepa, O., Cmunt, D., Grobarova, V.,Pazicky, S., Polachova, E., Abreu, C., Stransky, J., Koval, T., Duskova, J.,Zhao, Y.,Harlos, K., Hasek, J. Dohnalek, J., and Vanek, O.:

Structure of the human NK cell NKR-P1:LLT1 receptor: ligand complex reveals clustering in the immune synapse, Nature Comm. (2022)13:5022, https://doi.org/10.1038/s41467-022-32577-6

Research Highlights Archive


Selected publications

O. Gahura, et al.: An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases, Nature Communications, 13 (2022) 13, 10.1038/s41467-022-33588-z

M. Hluchy, et al.: CDK11 regulates pre-mRNA splicing by phosphorylation ofSF3B1, Nature, 36, 10.1038/s41586-022-05204-z

T. Smutna, et al.: A cytosolic ferredoxin-independent hydrogenase possibly mediates hydrogen uptake in Trichomonas vaginalis, Current Biology, 32 (2022) 124-+, 10.1016/j.cub.2021.10.050

Z. Dave, et al.: Lyn Phosphorylates and Controls ROR1 Surface Dynamics During Chemotaxis of CLL Cells, Front. Cell. Dev. Biol., 9 (2022) 11, 10.3389/fcell.2022.838871

V. Siahaan, et al.: Microtubule lattice spacing governs cohesive envelope formation of tau family proteins, Nat. Chem. Biol., 18 (2022) 1224-+, 10.1038/s41589-022-01096-2

P.R. Tharra, et al.: Short Synthesis of (+)-Actinobolin: Simple Entry to Complex Small-Molecule Inhibitors of Protein Synthesis, Angewandte Chemie-International Edition, (2022) 7, 10.1002/anie.202116520

M. Giladi, et al.: Structural basis for long-chain isoprenoid synthesis by cis-prenyltransferases, Sci. Adv., 8 (2022) 14, 10.1126/sciadv.abn1171

J. Blaha, et al.: Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse, Nature Communications, 13 (2022) 18, 10.1038/s41467-022-32577-6

M. Siborova, et al.: Tail proteins of phage SU10 reorganize into the nozzle for genome delivery, Nature Communications, 13 (2022) 13, 10.1038/s41467-022-33305-w

All publications
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