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Pleuger R, Cozma C, Hohoff S, Denkhaus C, Dudziak A, Kaschani F, Kaiser M, Musacchio A, Vetter IR, Westermann S. Microtubule end-on attachment maturation regulates Mps1 association with its kinetochore receptor. Curr Biol 2024; 34:2279-2293.e6. [PMID: 38776902 DOI: 10.1016/j.cub.2024.03.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/23/2024] [Accepted: 03/27/2024] [Indexed: 05/25/2024]
Abstract
Faithful chromosome segregation requires that sister chromatids establish bi-oriented kinetochore-microtubule attachments. The spindle assembly checkpoint (SAC) prevents premature anaphase onset with incomplete attachments. However, how microtubule attachment and checkpoint signaling are coordinated remains unclear. The conserved kinase Mps1 initiates SAC signaling by localizing transiently to kinetochores in prometaphase and is released upon bi-orientation. Using biochemistry, structure predictions, and cellular assays, we shed light on this dynamic behavior in Saccharomyces cerevisiae. A conserved N-terminal segment of Mps1 binds the neck region of Ndc80:Nuf2, the main microtubule receptor of kinetochores. Mutational disruption of this interface, located at the backside of the paired CH domains and opposite the microtubule-binding site, prevents Mps1 localization, eliminates SAC signaling, and impairs growth. The same interface of Ndc80:Nuf2 binds the microtubule-associated Dam1 complex. We demonstrate that the error correction kinase Ipl1/Aurora B controls the competition between Dam1 and Mps1 for the same binding site. Thus, binding of the Dam1 complex to Ndc80:Nuf2 may release Mps1 from the kinetochore to promote anaphase onset.
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Affiliation(s)
- Richard Pleuger
- Department of Molecular Genetics, Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany; Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Christian Cozma
- Department of Molecular Genetics, Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany; Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Simone Hohoff
- Department of Molecular Genetics, Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany; Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Christian Denkhaus
- Department of Molecular Genetics, Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany; Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Alexander Dudziak
- Department of Molecular Genetics, Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany; Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Farnusch Kaschani
- Department of Chemical Biology and ACE Analytical Core Facility Essen, Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany; Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Markus Kaiser
- Department of Chemical Biology and ACE Analytical Core Facility Essen, Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany; Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany
| | - Ingrid R Vetter
- Department of Mechanistic Cell Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Stefan Westermann
- Department of Molecular Genetics, Faculty of Biology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany; Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstrasse 5, 45117 Essen, Germany.
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2
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Power RM, Tschanz A, Zimmermann T, Ries J. Build and operation of a custom 3D, multicolor, single-molecule localization microscope. Nat Protoc 2024:10.1038/s41596-024-00989-x. [PMID: 38702387 DOI: 10.1038/s41596-024-00989-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/19/2024] [Indexed: 05/06/2024]
Abstract
Single-molecule localization microscopy (SMLM) enables imaging scientists to visualize biological structures with unprecedented resolution. Particularly powerful implementations of SMLM are capable of three-dimensional, multicolor and high-throughput imaging and can yield key biological insights. However, widespread access to these technologies is limited, primarily by the cost of commercial options and complexity of de novo development of custom systems. Here we provide a comprehensive guide for interested researchers who wish to establish a high-end, custom-built SMLM setup in their laboratories. We detail the initial configuration and subsequent assembly of the SMLM, including the instructions for the alignment of all the optical pathways, the software and hardware integration, and the operation of the instrument. We describe the validation steps, including the preparation and imaging of test and biological samples with structures of well-defined geometries, and assist the user in troubleshooting and benchmarking the system's performance. Additionally, we provide a walkthrough of the reconstruction of a super-resolved dataset from acquired raw images using the Super-resolution Microscopy Analysis Platform. Depending on the instrument configuration, the cost of the components is in the range US$95,000-180,000, similar to other open-source advanced SMLMs, and substantially lower than the cost of a commercial instrument. A builder with some experience of optical systems is expected to require 4-8 months from the start of the system construction to attain high-quality three-dimensional and multicolor biological images.
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Affiliation(s)
- Rory M Power
- EMBL Imaging Centre, EMBL Heidelberg, Heidelberg, Germany.
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Timo Zimmermann
- EMBL Imaging Centre, EMBL Heidelberg, Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany.
- Max Perutz Labs, Vienna Biocenter Campus, Vienna, Austria.
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Vienna, Austria.
- University of Vienna, Faculty of Physics, Vienna, Austria.
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Li S, Kasciukovic T, Tanaka TU. Kinetochore-microtubule error correction for biorientation: lessons from yeast. Biochem Soc Trans 2024; 52:29-39. [PMID: 38305688 PMCID: PMC10903472 DOI: 10.1042/bst20221261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024]
Abstract
Accurate chromosome segregation in mitosis relies on sister kinetochores forming stable attachments to microtubules (MTs) extending from opposite spindle poles and establishing biorientation. To achieve this, erroneous kinetochore-MT interactions must be resolved through a process called error correction, which dissolves improper kinetochore-MT attachment and allows new interactions until biorientation is achieved. The Aurora B kinase plays key roles in driving error correction by phosphorylating Dam1 and Ndc80 complexes, while Mps1 kinase, Stu2 MT polymerase and phosphatases also regulate this process. Once biorientation is formed, tension is applied to kinetochore-MT interaction, stabilizing it. In this review article, we discuss the mechanisms of kinetochore-MT interaction, error correction and biorientation. We focus mainly on recent insights from budding yeast, where the attachment of a single MT to a single kinetochore during biorientation simplifies the analysis of error correction mechanisms.
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Affiliation(s)
- Shuyu Li
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Taciana Kasciukovic
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Tomoyuki U. Tanaka
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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Muir KW, Batters C, Dendooven T, Yang J, Zhang Z, Burt A, Barford D. Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules. Science 2023; 382:1184-1190. [PMID: 38060647 PMCID: PMC7615550 DOI: 10.1126/science.adj8736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until biorientation is achieved. The structural basis for how kinetochore-mediated chromosome segregation is accomplished and regulated remains an outstanding question. In this work, we describe the cryo-electron microscopy structure of the budding yeast outer kinetochore Ndc80 and Dam1 ring complexes assembled onto microtubules. Complex assembly occurs through multiple interfaces, and a staple within Dam1 aids ring assembly. Perturbation of key interfaces suppresses yeast viability. Force-rupture assays indicated that this is a consequence of impaired kinetochore-microtubule attachment. The presence of error correction phosphorylation sites at Ndc80-Dam1 ring complex interfaces and the Dam1 staple explains how kinetochore-microtubule attachments are destabilized and reset.
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Affiliation(s)
- Kyle W. Muir
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christopher Batters
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Tom Dendooven
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alister Burt
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Barford
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
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Sankaranarayanan SR, Polisetty SD, Das K, Dumbrepatil A, Medina-Pritchard B, Singleton M, Jeyaprakash AA, Sanyal K. Functional plasticity in chromosome-microtubule coupling on the evolutionary time scale. Life Sci Alliance 2023; 6:e202201720. [PMID: 37793775 PMCID: PMC10551642 DOI: 10.26508/lsa.202201720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
The Dam1 complex is essential for mitotic progression across evolutionarily divergent fungi. Upon analyzing amino acid (aa) sequences of Dad2, a Dam1 complex subunit, we identified a conserved 10-aa-long Dad2 signature sequence (DSS). An arginine residue (R126) in the DSS is essential for viability in Saccharomyces cerevisiae that possesses point centromeres. The corresponding arginine residues are functionally important but not essential for viability in Candida albicans and Cryptococcus neoformans; both carry several kilobases long regional centromeres. The purified recombinant Dam1 complex containing either Dad2ΔDSS or Dad2R126A failed to bind microtubules (MTs) or form any visible rings like the WT complex. Intriguingly, functional analysis revealed that the requirement of the conserved arginine residue for chromosome biorientation and mitotic progression reduced with increasing centromere length. We propose that plasticity of the invariant arginine of Dad2 in organisms with regional centromeres is achieved by conditional elevation of the kinetochore protein(s) to enable multiple kinetochore MTs to bind to each chromosome. The capacity of a chromosome to bind multiple kinetochore MTs may mask the deleterious effects of such lethal mutations.
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Affiliation(s)
- Sundar Ram Sankaranarayanan
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Satya Dev Polisetty
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Kuladeep Das
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Arti Dumbrepatil
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Bethan Medina-Pritchard
- https://ror.org/01nrxwf90 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Martin Singleton
- https://ror.org/01nrxwf90 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - A Arockia Jeyaprakash
- https://ror.org/01nrxwf90 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
- Gene Center and Department of Biochemistry, Ludwig-Maximilian-Universität, Munich, Germany
| | - Kaustuv Sanyal
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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Dendooven T, Zhang Z, Yang J, McLaughlin SH, Schwab J, Scheres SHW, Yatskevich S, Barford D. Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere. SCIENCE ADVANCES 2023; 9:eadg7480. [PMID: 37506202 PMCID: PMC10381965 DOI: 10.1126/sciadv.adg7480] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) complex and the microtubule-binding outer kinetochore KNL1-MIS12-NDC80 (KMN) network. The budding yeast inner kinetochore also contains the DNA binding centromere-binding factor 1 (CBF1) and CBF3 complexes. We determined the cryo-electron microscopy structure of the yeast inner kinetochore assembled onto the centromere-specific centromere protein A nucleosomes (CENP-ANuc). This revealed a central CENP-ANuc with extensively unwrapped DNA ends. These free DNA duplexes bind two CCAN protomers, one of which entraps DNA topologically, positioned on the centromere DNA element I (CDEI) motif by CBF1. The two CCAN protomers are linked through CBF3 forming an arch-like configuration. With a structural mechanism for how CENP-ANuc can also be linked to KMN involving only CENP-QU, we present a model for inner kinetochore assembly onto a point centromere and how it organizes the outer kinetochore for chromosome attachment to the mitotic spindle.
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Affiliation(s)
| | | | - Jing Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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Virant D, Vojnovic I, Winkelmeier J, Endesfelder M, Turkowyd B, Lando D, Endesfelder U. Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color SMLM imaging. J Cell Biol 2023; 222:213836. [PMID: 36705602 PMCID: PMC9930162 DOI: 10.1083/jcb.202209096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/28/2023] Open
Abstract
The key to ensuring proper chromosome segregation during mitosis is the kinetochore (KT), a tightly regulated multiprotein complex that links the centromeric chromatin to the spindle microtubules and as such leads the segregation process. Understanding its architecture, function, and regulation is therefore essential. However, due to its complexity and dynamics, only its individual subcomplexes could be studied in structural detail so far. In this study, we construct a nanometer-precise in situ map of the human-like regional KT of Schizosaccharomyces pombe using multi-color single-molecule localization microscopy. We measure each protein of interest (POI) in conjunction with two references, cnp1CENP-A at the centromere and sad1 at the spindle pole. This allows us to determine cell cycle and mitotic plane, and to visualize individual centromere regions separately. We determine protein distances within the complex using Bayesian inference, establish the stoichiometry of each POI and, consequently, build an in situ KT model with unprecedented precision, providing new insights into the architecture.
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Affiliation(s)
- David Virant
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Ilijana Vojnovic
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Jannik Winkelmeier
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Marc Endesfelder
- https://ror.org/05591te55Institute for Assyriology and Hittitology, Ludwig-Maximilians-Universität München, München, Germany
| | - Bartosz Turkowyd
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - David Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ulrike Endesfelder
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany,Correspondence to Ulrike Endesfelder:
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8
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Čavka I, Power RM, Walsh D, Zimmermann T, Köhler S. Super-Resolution Microscopy of the Synaptonemal Complex within the Caenorhabditis elegans Germline. J Vis Exp 2022:10.3791/64363. [PMID: 36190293 PMCID: PMC7614930 DOI: 10.3791/64363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023] Open
Abstract
During meiosis, homologous chromosomes must recognize and adhere to one another to allow for their correct segregation. One of the key events that secures the interaction of homologous chromosomes is the assembly of the synaptonemal complex (SC) in meiotic prophase I. Even though there is little sequence homology between protein components within the SC among different species, the general structure of the SC has been highly conserved during evolution. In electron micrographs, the SC appears as a tripartite, ladder-like structure composed of lateral elements or axes, transverse filaments, and a central element. However, precisely identifying the localization of individual components within the complex by electron microscopy to determine the molecular structure of the SC remains challenging. By contrast, fluorescence microscopy allows for the identification of individual protein components within the complex. However, since the SC is only ~100 nm wide, its substructure cannot be resolved by diffraction-limited conventional fluorescence microscopy. Thus, determining the molecular architecture of the SC requires super-resolution light microscopy techniques such as structured illumination microscopy (SIM), stimulated-emission depletion (STED) microscopy, or single-molecule localization microscopy (SMLM). To maintain the structure and interactions of individual components within the SC, it is important to observe the complex in an environment that is close to its native environment in the germ cells. Therefore, we demonstrate an immunohistochemistry and imaging protocol that enables the study of the substructure of the SC in intact, extruded Caenorhabditis elegans germline tissue with SMLM and STED microscopy. Directly fixing the tissue to the coverslip reduces the movement of the samples during imaging and minimizes aberrations in the sample to achieve the high resolution necessary to visualize the substructure of the SC in its biological context.
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Affiliation(s)
- Ivana Čavka
- Cell Biology and Biophysics, European Molecular Biology Laboratory; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Rory M Power
- EMBL Imaging Centre, European Molecular Biology Laboratory
| | - Dietrich Walsh
- EMBL Imaging Centre, European Molecular Biology Laboratory
| | - Timo Zimmermann
- Cell Biology and Biophysics, European Molecular Biology Laboratory; EMBL Imaging Centre, European Molecular Biology Laboratory;
| | - Simone Köhler
- Cell Biology and Biophysics, European Molecular Biology Laboratory;
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