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Gewehr L, Junglas B, Jilly R, Franz J, Zhu WE, Weidner T, Bonn M, Sachse C, Schneider D. SynDLP is a dynamin-like protein of Synechocystis sp. PCC 6803 with eukaryotic features. Nat Commun 2023; 14:2156. [PMID: 37059718 PMCID: PMC10104851 DOI: 10.1038/s41467-023-37746-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
Dynamin-like proteins are membrane remodeling GTPases with well-understood functions in eukaryotic cells. However, bacterial dynamin-like proteins are still poorly investigated. SynDLP, the dynamin-like protein of the cyanobacterium Synechocystis sp. PCC 6803, forms ordered oligomers in solution. The 3.7 Å resolution cryo-EM structure of SynDLP oligomers reveals the presence of oligomeric stalk interfaces typical for eukaryotic dynamin-like proteins. The bundle signaling element domain shows distinct features, such as an intramolecular disulfide bridge that affects the GTPase activity, or an expanded intermolecular interface with the GTPase domain. In addition to typical GD-GD contacts, such atypical GTPase domain interfaces might be a GTPase activity regulating tool in oligomerized SynDLP. Furthermore, we show that SynDLP interacts with and intercalates into membranes containing negatively charged thylakoid membrane lipids independent of nucleotides. The structural characteristics of SynDLP oligomers suggest it to be the closest known bacterial ancestor of eukaryotic dynamin.
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Affiliation(s)
- Lucas Gewehr
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Benedikt Junglas
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany
- Institute for Biological Information Processing (IBI-6): Cellular Structural Biology, Jülich, Germany
| | - Ruven Jilly
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Johannes Franz
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Wenyu Eva Zhu
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Carsten Sachse
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany.
- Institute for Biological Information Processing (IBI-6): Cellular Structural Biology, Jülich, Germany.
- Department of Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, Germany.
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany.
- Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany.
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2
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Cyanobacterial membrane dynamics in the light of eukaryotic principles. Biosci Rep 2023; 43:232406. [PMID: 36602300 PMCID: PMC9950537 DOI: 10.1042/bsr20221269] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Intracellular compartmentalization is a hallmark of eukaryotic cells. Dynamic membrane remodeling, involving membrane fission/fusion events, clearly is crucial for cell viability and function, as well as membrane stabilization and/or repair, e.g., during or after injury. In recent decades, several proteins involved in membrane stabilization and/or dynamic membrane remodeling have been identified and described in eukaryotes. Yet, while typically not having a cellular organization as complex as eukaryotes, also bacteria can contain extra internal membrane systems besides the cytoplasmic membranes (CMs). Thus, also in bacteria mechanisms must have evolved to stabilize membranes and/or trigger dynamic membrane remodeling processes. In fact, in recent years proteins, which were initially defined being eukaryotic inventions, have been recognized also in bacteria, and likely these proteins shape membranes also in these organisms. One example of a complex prokaryotic inner membrane system is the thylakoid membrane (TM) of cyanobacteria, which contains the complexes of the photosynthesis light reaction. Cyanobacteria are evolutionary closely related to chloroplasts, and extensive remodeling of the internal membrane systems has been observed in chloroplasts and cyanobacteria during membrane biogenesis and/or at changing light conditions. We here discuss common principles guiding eukaryotic and prokaryotic membrane dynamics and the proteins involved, with a special focus on the dynamics of the cyanobacterial TMs and CMs.
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3
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Junglas B, Axt A, Siebenaller C, Sonel H, Hellmann N, Weber SAL, Schneider D. Membrane destabilization and pore formation induced by the Synechocystis IM30 protein. Biophys J 2022; 121:3411-3421. [PMID: 35986519 PMCID: PMC9515227 DOI: 10.1016/j.bpj.2022.08.014] [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: 03/18/2022] [Revised: 07/21/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
The inner membrane-associated protein of 30 kDa (IM30) is essential in chloroplasts and cyanobacteria. The spatio-temporal cellular localization of the protein appears to be highly dynamic and triggered by internal as well as external stimuli, mainly light intensity. The soluble fraction of the protein is localized in the cyanobacterial cytoplasm or the chloroplast stroma, respectively. Additionally, the protein attaches to the thylakoid membrane as well as to the chloroplast inner envelope or the cyanobacterial cytoplasmic membrane, respectively, especially under conditions of membrane stress. IM30 is involved in thylakoid membrane biogenesis and/or maintenance, where it either stabilizes membranes and/or triggers membrane-fusion processes. These apparently contradicting functions have to be tightly controlled and separated spatiotemporally in chloroplasts and cyanobacteria. IM30's fusogenic activity depends on Mg2+ binding to IM30; yet, it still is unclear how Mg2+-loaded IM30 interacts with membranes and promotes membrane fusion. Here, we show that the interaction of Mg2+ with IM30 results in increased binding of IM30 to native, as well as model, membranes. Via atomic force microscopy in liquid, IM30-induced bilayer defects were observed in solid-supported bilayers in the presence of Mg2+. These structures differ dramatically from the membrane-stabilizing carpet structures that were previously observed in the absence of Mg2+. Thus, Mg2+-induced alterations of the IM30 structure switch the IM30 activity from a membrane-stabilizing to a membrane-destabilizing function, a crucial step in membrane fusion.
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Affiliation(s)
- Benedikt Junglas
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Amelie Axt
- Max Planck-Institute for Polymer Research, Mainz, Germany; Institute of Physics, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Carmen Siebenaller
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hilal Sonel
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Stefan A L Weber
- Max Planck-Institute for Polymer Research, Mainz, Germany; Institute of Physics, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany; Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany.
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4
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Liu J, Tassinari M, Souza DP, Naskar S, Noel JK, Bohuszewicz O, Buck M, Williams TA, Baum B, Low HH. Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily. Cell 2021; 184:3660-3673.e18. [PMID: 34166615 PMCID: PMC8281802 DOI: 10.1016/j.cell.2021.05.041] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/24/2020] [Accepted: 05/25/2021] [Indexed: 12/31/2022]
Abstract
Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, using a combination of evolutionary and structural analyses, we show that these protein families are homologous and share a common ancient evolutionary origin that likely predates the last universal common ancestor. This homology is evident in cryo-electron microscopy structures of Vipp1 rings from the cyanobacterium Nostoc punctiforme presented over a range of symmetries. Each ring is assembled from rungs that stack and progressively tilt to form dome-shaped curvature. Assembly is facilitated by hinges in the Vipp1 monomer, similar to those in ESCRT-III proteins, which allow the formation of flexible polymers. Rings have an inner lumen that is able to bind and deform membranes. Collectively, these data suggest conserved mechanistic principles that underlie Vipp1, PspA, and ESCRT-III-dependent membrane remodeling across all domains of life.
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Affiliation(s)
- Jiwei Liu
- Department of Infectious Disease, Imperial College, London, UK
| | | | - Diorge P Souza
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Souvik Naskar
- Department of Infectious Disease, Imperial College, London, UK
| | - Jeffrey K Noel
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Martin Buck
- Department of Life Sciences, Imperial College, London, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Buzz Baum
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK; Institute for the Physics of Living Systems, University College London, London, UK.
| | - Harry H Low
- Department of Infectious Disease, Imperial College, London, UK.
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5
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Gupta TK, Klumpe S, Gries K, Heinz S, Wietrzynski W, Ohnishi N, Niemeyer J, Spaniol B, Schaffer M, Rast A, Ostermeier M, Strauss M, Plitzko JM, Baumeister W, Rudack T, Sakamoto W, Nickelsen J, Schuller JM, Schroda M, Engel BD. Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity. Cell 2021; 184:3643-3659.e23. [PMID: 34166613 DOI: 10.1016/j.cell.2021.05.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/16/2021] [Accepted: 05/10/2021] [Indexed: 12/21/2022]
Abstract
Vesicle-inducing protein in plastids 1 (VIPP1) is essential for the biogenesis and maintenance of thylakoid membranes, which transform light into life. However, it is unknown how VIPP1 performs its vital membrane-remodeling functions. Here, we use cryo-electron microscopy to determine structures of cyanobacterial VIPP1 rings, revealing how VIPP1 monomers flex and interweave to form basket-like assemblies of different symmetries. Three VIPP1 monomers together coordinate a non-canonical nucleotide binding pocket on one end of the ring. Inside the ring's lumen, amphipathic helices from each monomer align to form large hydrophobic columns, enabling VIPP1 to bind and curve membranes. In vivo mutations in these hydrophobic surfaces cause extreme thylakoid swelling under high light, indicating an essential role of VIPP1 lipid binding in resisting stress-induced damage. Using cryo-correlative light and electron microscopy (cryo-CLEM), we observe oligomeric VIPP1 coats encapsulating membrane tubules within the Chlamydomonas chloroplast. Our work provides a structural foundation for understanding how VIPP1 directs thylakoid biogenesis and maintenance.
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Affiliation(s)
- Tilak Kumar Gupta
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Sven Klumpe
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Karin Gries
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Steffen Heinz
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Wojciech Wietrzynski
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Norikazu Ohnishi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Justus Niemeyer
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Benjamin Spaniol
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Anna Rast
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Matthias Ostermeier
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Mike Strauss
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 17C, Canada
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Till Rudack
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, 44801 Bochum, Germany; Department of Biophysics, Faculty of Biology & Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Jörg Nickelsen
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Jan M Schuller
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, 35032 Marburg, Germany.
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany.
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Chemistry, Technical University of Munich, 85748 Garching, Germany.
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6
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Junglas B, Huber ST, Heidler T, Schlösser L, Mann D, Hennig R, Clarke M, Hellmann N, Schneider D, Sachse C. PspA adopts an ESCRT-III-like fold and remodels bacterial membranes. Cell 2021; 184:3674-3688.e18. [PMID: 34166616 DOI: 10.1016/j.cell.2021.05.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/01/2021] [Accepted: 05/26/2021] [Indexed: 12/31/2022]
Abstract
PspA is the main effector of the phage shock protein (Psp) system and preserves the bacterial inner membrane integrity and function. Here, we present the 3.6 Å resolution cryoelectron microscopy (cryo-EM) structure of PspA assembled in helical rods. PspA monomers adopt a canonical ESCRT-III fold in an extended open conformation. PspA rods are capable of enclosing lipids and generating positive membrane curvature. Using cryo-EM, we visualized how PspA remodels membrane vesicles into μm-sized structures and how it mediates the formation of internalized vesicular structures. Hotspots of these activities are zones derived from PspA assemblies, serving as lipid transfer platforms and linking previously separated lipid structures. These membrane fusion and fission activities are in line with the described functional properties of bacterial PspA/IM30/LiaH proteins. Our structural and functional analyses reveal that bacterial PspA belongs to the evolutionary ancestry of ESCRT-III proteins involved in membrane remodeling.
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Affiliation(s)
- Benedikt Junglas
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Stefan T Huber
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thomas Heidler
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Lukas Schlösser
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Daniel Mann
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Raoul Hennig
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Mairi Clarke
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; Institute of Molecular Physiology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany.
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Department of Biology, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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7
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Siebenaller C, Schlösser L, Junglas B, Schmidt-Dengler M, Jacob D, Hellmann N, Sachse C, Helm M, Schneider D. Binding and/or hydrolysis of purine-based nucleotides is not required for IM30 ring formation. FEBS Lett 2021; 595:1876-1885. [PMID: 34060653 DOI: 10.1002/1873-3468.14140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/30/2021] [Accepted: 05/20/2021] [Indexed: 11/09/2022]
Abstract
IM30, the inner membrane-associated protein of 30 kDa, is conserved in cyanobacteria and chloroplasts. Although its exact physiological function is still mysterious, IM30 is clearly essential for thylakoid membrane biogenesis and/or dynamics. Recently, a cryptic IM30 GTPase activity has been reported, albeit thus far no physiological function has been attributed to this. Yet, it is still possible that GTP binding/hydrolysis affects formation of the prototypical large homo-oligomeric IM30 ring and rod structures. Here, we show that the Synechocystis sp. PCC 6803 IM30 protein in fact is an NTPase that hydrolyzes GTP and ATP, but not CTP or UTP, with about identical rates. While IM30 forms large oligomeric ring complexes, nucleotide binding and/or hydrolysis are clearly not required for ring formation.
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Affiliation(s)
- Carmen Siebenaller
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany
| | - Lukas Schlösser
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany
| | - Benedikt Junglas
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany.,Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Germany
| | - Martina Schmidt-Dengler
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Germany
| | - Dominik Jacob
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Germany
| | - Mark Helm
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany.,Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Germany
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