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Instruments / Technical Area	Publication Details	Published
	The single-particle, clusters and biomolecules and serial femtosecond crystallography instrument of the European X-ray Free-Electron Laser: Interaction region downstream at atmospheric pressure (IRD) Adam Round , Pierre Aller , Richard Bean , Johan Bielecki , Agata Butryn , Nicholas E. Devenish , Raphael De Wijn , Thomas Dietze , Katerina Doerner , Fabio Dall'Antonia , Gabriele Giovanetti , Huijong Han , Vincent Hennicke , Chan Kim , Yoonhee Kim , Marco Kloos , Jayanath C. P. Koliyadu , Gabriel Leen , Romain Letrun , Luis Lopez Morillo , Allen M. Orville , Tim Pakendorf , Marco Ramilli , Nadja Reimers , Patrick Reinke , Juan Sanchez-Weatherby , Tokushi Sato , Robin Schubert , Joachim Schulz , Cedric Signe Takem , Marcin Sikorski , Prasad Thute , Fabian Trost , Oleksii Turkot , Patrik Vagovic , Mohammad Vakili , Raul Villanueva Guerrero , Henry N. Chapman , Alke Meents , Serguei Molodtsov , Sakura Pascarelli , Thomas Tschentschera , Adrian Mancuso , Pontus Fischer , Sebastian Guenther Journal Of Synchrotron Radiation 33 DOI: 10.1107/S1600577525008999 Open Access Show Abstract ▼ Abstract: The Single-Particle, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) scientific instrument at the European X-Ray Free-Electron Laser (EuXFEL) became operational with user experiments in September 2017. The unique properties and capabilities of the EuXFEL, enabling megahertz data collection rates, provide more rapid data collection with improved statistics compared with other XFEL facilities. This improves the feasibility of obtaining multiple data points in time-resolved experiments and hence enables the observation of reactions in greater detail (molecular movies). In collaboration with the SFX User Consortium (SFX UC), the SPB/SFX instrument was designed to further increase user access and research outcomes. Focusing the pulses downstream of the first interaction region [described previously (Mancuso et al., 2019)], a second experiment plane is enabled, which allows for greater optimization and more efficient usage of available beam time. Additionally, the SFX UC provided further instrumentation to provide improved capabilities on SPB/SFX. The aim for additional and extended functionality for the second interaction region was to enable sample-efficient data collection at atmospheric pressure in an environment where the sample temperature and humidity can be controlled. This paper describes the extended capabilities of the downstream interaction region of the SPB/SFX instrument and its major components, in particular its X-ray focusing optics, vacuum to atmospheric pressure out-coupling, available sample delivery methods and 2D detector, and the supporting optical laser systems for pump–probe experiments.	Nov 2025
	Pr and Pfr structures of plant phytochrome A Soshichiro Nagano , David Von Stetten , Kaoling Guan , Peng-Yuan Chen , Chen Song , Thomas Barends , Manfred S. Weiss , Christian G. Feiler , Katerina Dörner , Iñaki De Diego Martinez , Robin Schubert , Johan Bielecki , Lea Brings , Huijong Han , Konstantin Kharitonov , Chan Kim , Marco Kloos , Jayanath C. P. Koliyadu , Faisal H. M. Koua , Ekaterina Round , Abhisakh Sarma , Tokushi Sato , Christina Schmidt , Joana Valerio , Agnieszka Wrona , Joachim Schulz , Raphael De Wijn , Romain Letrun , Richard Bean , Adrian Mancuso , Karsten Heyne , Jon Hughes Nature Communications 16 DOI: 10.1038/s41467-025-60738-w Open Access Show Abstract ▼ Abstract: Phytochromes are biliprotein photoreceptors widespread amongst microorganisms and ubiquitous in plants where they control developmental processes as diverse as germination, stem elongation and floral induction through the photoconversion of inactive Pr to the Pfr signalling state. Here we report crystal structures of the chromophore-binding module of soybean phytochrome A, including ~2.2 Å XFEL structures of Pr and Pfr at ambient temperature and high resolution cryogenic structures of Pr. In the Pfr structure, the chromophore is exposed to the medium, the D-ring remaining α-facial following the likely clockwise photoflip. The chromophore shifts within its pocket, while its propionate side chains, their partners as well as three neighbouring tyrosines shift radically. Helices near the chromophore show substantial shifts that might represent components of the light signal. These changes reflect those in bacteriophytochromes despite their quite different signalling mechanisms, implying that fundamental aspects of phytochrome photoactivation have been repurposed for photoregulation in the eukaryotic plant.	Jun 2025
	Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease Vasundara Srinivasan , Hévila Brognaro , Prince R. Prabhu , Edmarcia Elisa De Souza , Sebastian Günther , Patrick Y. A. Reinke , Thomas J. Lane , Helen Ginn , Huijong Han , Wiebke Ewert , Janina Sprenger , Faisal H. M. Koua , Sven Falke , Nadine Werner , Hina Andaleeb , Najeeb Ullah , Bruno Alves Franca , Mengying Wang , Angélica Luana C. Barra , Markus Perbandt , Martin Schwinzer , Christina Schmidt , Lea Brings , Kristina Lorenzen , Robin Schubert , Rafael Rahal Guaragna Machado , Erika Donizette Candido , Danielle Bruna Leal Oliveira , Edison Luiz Durigon , Stephan Niebling , Angelica Struve Garcia , Oleksandr Yefanov , Julia Lieske , Luca Gelisio , Martin Domaracky , Philipp Middendorf , Michael Groessler , Fabian Trost , Marina Galchenkova , Aida Rahmani Mashhour , Sofiane Saouane , Johanna Hakanpää , Markus Wolf , Maria Garcia Alai , Dusan Turk , Arwen R. Pearson , Henry N. Chapman , Winfried Hinrichs , Carsten Wrenger , Alke Meents , Christian Betzel Communications Biology 5 DOI: 10.1038/s42003-022-03737-7 Open Access Show Abstract ▼ Abstract: SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host’s innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.	Aug 2022
	X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease Sebastian Gunther , Patrick Y. A. Reinke , Yaiza Fernández-García , Julia Lieske , Thomas J. Lane , Helen M. Ginn , Faisal H. M. Koua , Christiane Ehrt , Wiebke Ewert , Dominik Oberthuer , Oleksandr Yefanov , Susanne Meier , Kristina Lorenzen , Boris Krichel , Janine-Denise Kopicki , Luca Gelisio , Wolfgang Brehm , Ilona Dunkel , Brandon Seychell , Henry Gieseler , Brenna Norton-Baker , Beatriz Escudero-Pérez , Martin Domaracky , Sofiane Saouane , Alexandra Tolstikova , Thomas A. White , Anna Hänle , Michael Groessler , Holger Fleckenstein , Fabian Trost , Marina Galchenkova , Yaroslav Gevorkov , Chufeng Li , Salah Awel , Ariana Peck , Miriam Barthelmess , Frank Schluenzen , Paulraj Lourdu Xavier , Nadine Werner , Hina Andaleeb , Najeeb Ullah , Sven Falke , Vasundara Srinivasan , Bruno Alves França , Martin Schwinzer , Hévila Brognaro , Cromarte Rogers , Diogo Melo , Joanna J. Zaitseva-Doyle , Juraj Knoska , Gisel E. Peña-Murillo , Aida Rahmani Mashhour , Vincent Hennicke , Pontus Fischer , Johanna Hakanpää , Jan Meyer , Philip Gribbon , Bernhard Ellinger , Maria Kuzikov , Markus Wolf , Andrea R. Beccari , Gleb Bourenkov , David Von Stetten , Guillaume Pompidor , Isabel Bento , Saravanan Panneerselvam , Ivars Karpics , Thomas R. Schneider , Maria Marta Garcia-Alai , Stephan Niebling , Christian Günther , Christina Schmidt , Robin Schubert , Huijong Han , Juliane Boger , Diana C. F. Monteiro , Linlin Zhang , Xinyuanyuan Sun , Jonathan Pletzer-Zelgert , Jan Wollenhaupt , Christian G. Feiler , Manfred S. Weiss , Eike-Christian Schulz , Pedram Mehrabi , Katarina Karničar , Aleksandra Usenik , Jure Loboda , Henning Tidow , Ashwin Chari , Rolf Hilgenfeld , Charlotte Uetrecht , Russell Cox , Andrea Zaliani , Tobias Beck , Matthias Rarey , Stephan Günther , Dusan Turk , Winfried Hinrichs , Henry N. Chapman , Arwen R. Pearson , Christian Betzel , Alke Meents Science DOI: 10.1126/science.abf7945 Open Access Show Abstract ▼ Abstract: The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.	Apr 2021
I03-Macromolecular Crystallography	Megahertz serial crystallography Max O. Wiedorn , Dominik Oberthuer , Richard Bean , Robin Schubert , Nadine Werner , Brian Abbey , Martin Aepfelbacher , Luigi Adriano , Aschkan Allahgholi , Nasser Al-Qudami , Jakob Andreasson , Steve Aplin , Salah Awel , Kartik Ayyer , Saša Bajt , Imrich Barák , Sadia Bari , Johan Bielecki , Sabine Botha , Djelloul Boukhelef , Wolfgang Brehm , Sandor Brockhauser , Igor Cheviakov , Matthew A. Coleman , Francisco Cruz-Mazo , Cyril Danilevski , Connie Darmanin , R. Bruce Doak , Martin Domaracky , Katerina Dörner , Yang Du , Hans Fangohr , Holger Fleckenstein , Matthias Frank , Petra Fromme , Alfonso M. Gañán-Calvo , Yaroslav Gevorkov , Klaus Giewekemeyer , Helen Mary Ginn , Heinz Graafsma , Rita Graceffa , Dominic Greiffenberg , Lars Gumprecht , Peter Göttlicher , Janos Hajdu , Steffen Hauf , Michael Heymann , Susannah Holmes , Daniel A. Horke , Mark S. Hunter , Siegfried Imlau , Alexander Kaukher , Yoonhee Kim , Alexander Klyuev , Juraj Knoška , Bostjan Kobe , Manuela Kuhn , Christopher Kupitz , Jochen Küpper , Janine Mia Lahey-Rudolph , Torsten Laurus , Karoline Le Cong , Romain Letrun , P. Lourdu Xavier , Luis Maia , Filipe R. N. C. Maia , Valerio Mariani , Marc Messerschmidt , Markus Metz , Davide Mezza , Thomas Michelat , Grant Mills , Diana C. F. Monteiro , Andrew Morgan , Kerstin Mühlig , Anna Munke , Astrid Münnich , Julia Nette , Keith A. Nugent , Theresa Nuguid , Allen M. Orville , Suraj Pandey , Gisel Pena , Pablo Villanueva-Perez , Jennifer Poehlsen , Gianpietro Previtali , Lars Redecke , Winnie Maria Riekehr , Holger Rohde , Adam Round , Tatiana Safenreiter , Iosifina Sarrou , Tokushi Sato , Marius Schmidt , Bernd Schmitt , Robert Schönherr , Joachim Schulz , Jonas A. Sellberg , M. Marvin Seibert , Carolin Seuring , Megan L. Shelby , Robert L. Shoeman , Marcin Sikorski , Alessandro Silenzi , Claudiu A. Stan , Xintian Shi , Stephan Stern , Jola Sztuk-Dambietz , Janusz Szuba , Aleksandra Tolstikova , Martin Trebbin , Ulrich Trunk , Patrik Vagovic , Thomas Ve , Britta Weinhausen , Thomas A. White , Krzysztof Wrona , Chen Xu , Oleksandr Yefanov , Nadia Zatsepin , Jiaguo Zhang , Markus Perbandt , Adrian P. Mancuso , Christian Betzel , Henry Chapman , Anton Barty Nature Communications 9 DOI: 10.1038/s41467-018-06156-7 Open Access Show Abstract ▼ Abstract: The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.	Oct 2018

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