{"entity": "researcher", "timestamp": "2026-07-20T13:16:35.529Z", "family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "affiliations": ["Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/df2317a49446495a8839262b9f58fe38.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/df2317a49446495a8839262b9f58fe38"}}, "publications": [{"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": "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"}, {"entity": "publication", "iuid": "2169891b741d469abe009aa481604680", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2169891b741d469abe009aa481604680.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2169891b741d469abe009aa481604680"}}, "title": "Structures of the human mitochondrial ribosome in native states of assembly", "authors": [{"family": "Brown", "given": "Alan", "initials": "A", "orcid": "0000-0002-0021-0476", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bb38a7f086247fdb2e2b3bfb80dae1e.json"}}, {"family": "Rathore", "given": "Sorbhi", "initials": "S", "orcid": "0000-0001-9178-1006", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2293f9f60f44cfa47f1e3691c1309d.json"}}, {"family": "Kimanius", "given": "Dari", "initials": "D", "orcid": "0000-0002-2662-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/df2317a49446495a8839262b9f58fe38.json"}}, {"family": "Aibara", "given": "Shintaro", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d66746c4bec5414da78b2a325a13328f.json"}}, {"family": "Bai", "given": "Xiao chen", "initials": "Xc"}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}, {"family": "Amunts", "given": "Alexey", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Ramakrishnan", "given": "V", "initials": "V", "orcid": "0000-0002-4699-2194", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c59648b4e90409da2fcd0c4ae0355c6.json"}}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "24", "issn": "1545-9993", "issue": "10", "pages": "866-869", "title": "Nat Struct Mol Biol", "issn-l": "1545-9985"}, "abstract": "Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive. Here, we report the structures of two late-stage assembly intermediates of the human mitoribosomal large subunit (mt-LSU) isolated from a native pool within a human cell line and solved by cryo-EM to \u223c3-\u00c5 resolution. Comparison of the structures reveals insights into the timing of rRNA folding and protein incorporation during the final steps of ribosomal maturation and the evolutionary adaptations that are required to preserve biogenesis after the structural diversification of mitoribosomes. Furthermore, the structures redefine the ribosome silencing factor (RsfS) family as multifunctional biogenesis factors and identify two new assembly factors (L0R8F8 and mt-ACP) not previously implicated in mitoribosomal biogenesis.", "doi": "10.1038/nsmb.3464", "pmid": "28892042", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "mid", "key": "EMS73849"}, {"db": "pmc", "key": "PMC5633077"}, {"db": "pii", "key": "nsmb.3464"}], "notes": [], "created": "2017-10-16T16:18:18.520Z", "modified": "2023-12-04T10:11:28.653Z"}]}