{"entity": "researcher", "timestamp": "2026-07-17T08:45:24.292Z", "family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0003-1333-5398", "affiliations": ["Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad"}}, "publications": [{"entity": "publication", "iuid": "2ad60769fa49433e9865d2124a284a9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ad60769fa49433e9865d2124a284a9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ad60769fa49433e9865d2124a284a9b"}}, "title": "Structure and dynamics of differential ligand binding in the human \u03c1-type GABAA receptor.", "authors": [{"family": "Cowgill", "given": "John", "initials": "J"}, {"family": "Fan", "given": "Chen", "initials": "C"}, {"family": "Haloi", "given": "Nandan", "initials": "N"}, {"family": "Tobiasson", "given": "Victor", "initials": "V", "orcid": "0000-0001-8920-017X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5208789057a94d0d9575476bf9c88d5a.json"}}, {"family": "Zhuang", "given": "Yuxuan", "initials": "Y"}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ"}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}}], "type": "journal article", "published": "2023-11-01", "journal": {"title": "Neuron", "issn": "1097-4199", "volume": "111", "issue": "21", "pages": "3450-3464.e5", "issn-l": "0896-6273"}, "abstract": "The neurotransmitter \u03b3-aminobutyric acid (GABA) drives critical inhibitory processes in and beyond the nervous system, partly via ionotropic type-A receptors (GABAARs). Pharmacological properties of \u03c1-type GABAARs are particularly distinctive, yet the structural basis for their specialization remains unclear. Here, we present cryo-EM structures of a lipid-embedded human \u03c11 GABAAR, including a partial intracellular domain, under apo, inhibited, and desensitized conditions. An apparent resting state, determined first in the absence of modulators, was recapitulated with the specific inhibitor (1,2,5,6-tetrahydropyridin-4-yl)methylphosphinic acid and blocker picrotoxin and provided a rationale for bicuculline insensitivity. Comparative structures, mutant recordings, and molecular simulations with and without GABA further explained the sensitized but slower activation of \u03c11 relative to canonical subtypes. Combining GABA with picrotoxin also captured an apparent uncoupled intermediate state. This work reveals structural mechanisms of gating and modulation with applications to \u03c1-specific pharmaceutical design and to our biophysical understanding of ligand-gated ion channels.", "doi": "10.1016/j.neuron.2023.08.006", "pmid": "37659407", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "S0896-6273(23)00587-1"}], "notes": [], "created": "2023-09-19T08:21:37.127Z", "modified": "2023-12-04T09:50:38.972Z"}, {"entity": "publication", "iuid": "f5382fa2acda4d9c8e8301fb63479538", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5382fa2acda4d9c8e8301fb63479538.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5382fa2acda4d9c8e8301fb63479538"}}, "title": "\u03b1-Synuclein promotes IAPP fibril formation in vitro and \u03b2-cell amyloid formation in vivo in mice.", "authors": [{"family": "Mucibabic", "given": "Marija", "initials": "M"}, {"family": "Steneberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Lidh", "given": "Emmelie", "initials": "E"}, {"family": "Straseviciene", "given": "Jurate", "initials": "J"}, {"family": "Ziolkowska", "given": "Agnieszka", "initials": "A", "orcid": "0000-0002-4262-7106", "researcher": {"href": "https://publications.scilifelab.se/researcher/1355ff26d9cf4626bad7b3b93bf0a90d.json"}}, {"family": "Dahl", "given": "Ulf", "initials": "U"}, {"family": "Lindahl", "given": "Emma", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}}, {"family": "Edlund", "given": "Helena", "initials": "H"}], "type": "journal article", "published": "2020-11-24", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "20438", "issn-l": "2045-2322"}, "abstract": "Type 2 diabetes (T2D), alike Parkinson's disease (PD), belongs to the group of protein misfolding diseases (PMDs), which share aggregation of misfolded proteins as a hallmark. Although the major aggregating peptide in \u03b2-cells of T2D patients is Islet Amyloid Polypeptide (IAPP), alpha-synuclein (\u03b1Syn), the aggregating peptide in substantia nigra neurons of PD patients, is expressed also in \u03b2-cells. Here we show that \u03b1Syn, encoded by Snca, is a component of amyloid extracted from pancreas of transgenic mice overexpressing human IAPP (denoted hIAPPtg mice) and from islets of T2D individuals. Notably, \u03b1Syn dose-dependently promoted IAPP fibril formation in vitro and tail-vein injection of \u03b1Syn in hIAPPtg mice enhanced \u03b2-cell amyloid formation in vivo whereas \u03b2-cell amyloid formation was reduced in hIAPPtg mice on a Snca -/- background. Taken together, our findings provide evidence that \u03b1Syn and IAPP co-aggregate both in vitro and in vivo, suggesting a role for \u03b1Syn in \u03b2-cell amyloid formation.", "doi": "10.1038/s41598-020-77409-z", "pmid": "33235246", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-77409-z"}, {"db": "pmc", "key": "PMC7686322"}], "notes": [], "created": "2020-12-10T11:07:23.272Z", "modified": "2023-12-04T10:15:38.252Z"}, {"entity": "publication", "iuid": "f0d8698f1e574a76ae40262eb1688cc2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0d8698f1e574a76ae40262eb1688cc2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0d8698f1e574a76ae40262eb1688cc2"}}, "title": "Development of basic building blocks for cryo-EM: the emcore and emvis software libraries.", "authors": [{"family": "de la Rosa-Trev\u00edn", "given": "Jos\u00e9 Miguel", "initials": "JM", "orcid": "0000-0002-3320-1269", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c797d9907249f0bb608c1340ac6f5c.json"}}, {"family": "Hern\u00e1ndez Viga", "given": "Pedro Alberto", "initials": "PA"}, {"family": "Ot\u00f3n", "given": "Joaqu\u00edn", "initials": "J", "orcid": "0000-0002-2195-4730", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e00da8089474e7d86c26014cab70f9d.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}}], "type": "journal article", "published": "2020-04-01", "journal": {"title": "Acta Crystallogr D Struct Biol", "issn": "2059-7983", "issn-l": "2059-7983", "volume": "76", "issue": "Pt 4", "pages": "350-356"}, "abstract": "Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionality organized in modular components that other developers can reuse to implement new algorithms or build graphical applications. An additional aim is to showcase the importance of following established practices in software engineering, with the hope that this could be a first step towards a more standardized way of developing and distributing software in the field.", "doi": "10.1107/S2059798320003769", "pmid": "32254059", "labels": {"Cryo-EM": "Technology development"}, "xrefs": [{"db": "pii", "key": "S2059798320003769"}, {"db": "pmc", "key": "PMC7137102"}], "notes": [], "created": "2020-09-17T13:00:31.770Z", "modified": "2023-12-04T10:07:08.601Z"}, {"entity": "publication", "iuid": "07fd46e34e6b43b2b1385a5be8d527c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07fd46e34e6b43b2b1385a5be8d527c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07fd46e34e6b43b2b1385a5be8d527c2"}}, "title": "New tools for automated high-resolution cryo-EM structure determination in RELION-3", "authors": [{"family": "Zivanov", "given": "Jasenko", "initials": "J"}, {"family": "Nakane", "given": "Takanori", "initials": "T"}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5434ab128e04b2b951abbbea77221c8.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/df2317a49446495a8839262b9f58fe38.json"}}, {"family": "Hagen", "given": "Wim JH", "initials": "WJ"}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}}, {"family": "Scheres", "given": "Sjors HW", "initials": "SH"}], "type": "journal-article", "published": "2018-11-09", "journal": {"volume": "7", "issn": "2050-084X", "issue": null, "pages": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": null, "doi": "10.7554/elife.42166", "pmid": "30412051", "labels": {"Cryo-EM": "Technology development"}, "xrefs": [], "notes": [], "created": "2018-12-05T16:06:40.997Z", "modified": "2023-12-04T10:13:28.691Z"}, {"entity": "publication", "iuid": "92cab8743c914793addeffdf3501813d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92cab8743c914793addeffdf3501813d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92cab8743c914793addeffdf3501813d"}}, "title": "Using Scipion for stream image processing at Cryo-EM facilities", "authors": [{"family": "G\u00f3mez-Blanco", "given": "J", "initials": "J"}, {"family": "de la Rosa-Trev\u00edn", "given": "J M", "initials": "JM", "orcid": "0000-0002-3320-1269", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c797d9907249f0bb608c1340ac6f5c.json"}}, {"family": "Marabini", "given": "R", "initials": "R"}, {"family": "del Cano", "given": "L", "initials": "L"}, {"family": "Jim\u00e9nez", "given": "A", "initials": "A"}, {"family": "Mart\u00ednez", "given": "M", "initials": "M"}, {"family": "Melero", "given": "R", "initials": "R"}, {"family": "Majtner", "given": "T", "initials": "T"}, {"family": "Maluenda", "given": "D", "initials": "D"}, {"family": "Mota", "given": "J", "initials": "J"}, {"family": "Rancel", "given": "Y", "initials": "Y"}, {"family": "Ram\u00edrez-Aportela", "given": "E", "initials": "E"}, {"family": "Vilas", "given": "J L", "initials": "JL"}, {"family": "Carroni", "given": "M", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Fleischmann", "given": "S", "initials": "S"}, {"family": "Lindahl", "given": "E", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}}, {"family": "Ashton", "given": "A W", "initials": "AW"}, {"family": "Basham", "given": "M", "initials": "M"}, {"family": "Clare", "given": "D K", "initials": "DK"}, {"family": "Savage", "given": "K", "initials": "K"}, {"family": "Siebert", "given": "C A", "initials": "CA"}, {"family": "Sharov", "given": "G G", "initials": "GG"}, {"family": "Sorzano", "given": "C O S", "initials": "COS"}, {"family": "Conesa", "given": "P", "initials": "P"}, {"family": "Carazo", "given": "J M", "initials": "JM"}], "type": "journal-article", "published": "2018-10-00", "journal": {"volume": null, "issn": "1047-8477", "issue": null, "pages": null, "title": "Journal of Structural Biology", "issn-l": "1047-8477"}, "abstract": null, "doi": "10.1016/j.jsb.2018.10.001", "pmid": "30296492", "labels": {"Cryo-EM": "Technology development"}, "xrefs": [], "notes": [], "created": "2018-10-19T20:43:58.020Z", "modified": "2023-12-04T10:06:41.293Z"}, {"entity": "publication", "iuid": "0e147a5dedd845faac46f7a0cdbb4de5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e147a5dedd845faac46f7a0cdbb4de5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e147a5dedd845faac46f7a0cdbb4de5"}}, "title": "Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor", "authors": [{"family": "Perez Boerema", "given": "Annemarie", "initials": "A"}, {"family": "Aibara", "given": "Shintaro", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d66746c4bec5414da78b2a325a13328f.json"}}, {"family": "Paul", "given": "Bijoya", "initials": "B"}, {"family": "Tobiasson", "given": "Victor", "initials": "V", "orcid": "0000-0001-8920-017X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5208789057a94d0d9575476bf9c88d5a.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/df2317a49446495a8839262b9f58fe38.json"}}, {"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5434ab128e04b2b951abbbea77221c8.json"}}, {"family": "Wallden", "given": "Karin", "initials": "K"}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}}, {"family": "Amunts", "given": "A", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal-article", "published": "2018-04-02", "journal": {"volume": "4", "issn": "2055-0278", "issue": "4", "pages": "212-217", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": "Oxygenic photosynthesis produces oxygen and builds a variety of organic compounds, changing the chemistry of the air, the sea and fuelling the food chain on our planet. The photochemical reactions underpinning this process in plants take place in the chloroplast. Chloroplasts evolved ~1.2 billion years ago from an engulfed primordial diazotrophic cyanobacterium, and chlororibosomes are responsible for synthesis of the core proteins driving photochemical reactions. Chlororibosomal activity is spatiotemporally coupled to the synthesis and incorporation of functionally essential co-factors, implying the presence of chloroplast-specific regulatory mechanisms and structural adaptation of the chlororibosome1,2. Despite recent structural information3-6, some of these aspects remained elusive. To provide new insights into the structural specialities and evolution, we report a comprehensive analysis of the 2.9-3.1 \u00c5 resolution electron cryo-microscopy structure of the spinach chlororibosome in complex with its recycling factor and hibernation-promoting factor. The model reveals a prominent channel extending from the exit tunnel to the chlororibosome exterior, structural re-arrangements that lead to increased surface area for translocon binding, and experimental evidence for parallel and convergent evolution of chloro- and mitoribosomes.", "doi": "10.1038/s41477-018-0129-6", "pmid": "29610536", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41477-018-0129-6"}], "notes": [], "created": "2018-04-11T08:19:19.613Z", "modified": "2023-12-04T10:12:49.407Z"}, {"entity": "publication", "iuid": "8ce18e23922244cb80ddedc4e8cf83c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ce18e23922244cb80ddedc4e8cf83c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ce18e23922244cb80ddedc4e8cf83c2"}}, "title": "Cryo-EM reconstruction of the chlororibosome to 3.2 \u00c5 resolution within 24 h", "authors": [{"family": "Forsberg", "given": "Bj\u00f6rn O", "initials": "BO", "orcid": "0000-0002-6247-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5434ab128e04b2b951abbbea77221c8.json"}}, {"family": "Aibara", "given": "Shintaro", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d66746c4bec5414da78b2a325a13328f.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/df2317a49446495a8839262b9f58fe38.json"}}, {"family": "Paul", "given": "Bijoya", "initials": "B"}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0003-1333-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/51600cedcf044bdda0f677deaeaf9fad.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}], "type": "journal-article", "published": "2017-11-01", "journal": {"volume": "4", "issn": "2052-2525", "issue": "6", "pages": "723-727", "title": "Int Union Crystallogr J IUCr J Int Union Cryst J IUCrJ", "issn-l": "2052-2525"}, "abstract": "The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on-the-fly workflows that connect data collection with three-dimensional reconstruction would be valuable for more efficient use of cryo-EM and its application as a sample-screening tool. Here, accelerated on-the-fly analysis is reported with optimized organization of the data-processing tools, image acquisition and particle alignment that make it possible to reconstruct the three-dimensional density of the 70S chlororibosome to 3.2 \u00c5 resolution within 24 h of tissue harvesting. It is also shown that it is possible to achieve even faster processing at comparable quality by imposing some limits to data use, as illustrated by a 3.7 \u00c5 resolution map that was obtained in only 80 min on a desktop computer. These on-the-fly methods can be employed as an assessment of data quality from small samples and extended to high-throughput approaches.", "doi": "10.1107/s205225251701226x", "pmid": "29123673", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5668856"}, {"db": "pii", "key": "kf5004"}], "notes": [], "created": "2017-10-16T16:16:22.554Z", "modified": "2023-06-19T08:55:09.359Z"}]}