{"entity": "journal", "iuid": "68f1014ad5944c88b501d5e51b8960d8", "timestamp": "2026-07-13T10:09:31.100Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Acta%20Crystallogr%20D%20Struct%20Biol.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Acta%20Crystallogr%20D%20Struct%20Biol"}}, "title": "Acta Crystallogr D Struct Biol", "issn": "2059-7983", "issn-l": "2059-7983", "publications_count": 5, "publications": [{"entity": "publication", "iuid": "a5edd32e34ca4d70895006cf2d3f8d72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5edd32e34ca4d70895006cf2d3f8d72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5edd32e34ca4d70895006cf2d3f8d72"}}, "title": "Microcrystal electron diffraction structure of Toll-like receptor 2 TIR-domain-nucleated MyD88 TIR-domain higher-order assembly.", "authors": [{"family": "Li", "given": "Y", "initials": "Y", "orcid": "0000-0001-8317-824X", "researcher": {"href": "https://publications.scilifelab.se/researcher/19c182a9efbd438787c46812f3e0bd98.json"}}, {"family": "Pacoste", "given": "L C", "initials": "LC", "orcid": "0009-0005-6090-8736", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d78c5b22b984ee5b2803a2bfe8458a3.json"}}, {"family": "Gu", "given": "W", "initials": "W", "orcid": "0000-0002-1185-3557", "researcher": {"href": "https://publications.scilifelab.se/researcher/19785d2333584427b5211b7cc60867bb.json"}}, {"family": "Thygesen", "given": "S J", "initials": "SJ", "orcid": "0000-0002-7512-4097", "researcher": {"href": "https://publications.scilifelab.se/researcher/e41f6ad37780455983f73db785903907.json"}}, {"family": "Stacey", "given": "K J", "initials": "KJ", "orcid": "0000-0002-3992-7802", "researcher": {"href": "https://publications.scilifelab.se/researcher/af54c84a4bf34673be1efdecbcf701dd.json"}}, {"family": "Ve", "given": "T", "initials": "T", "orcid": "0000-0002-0113-1905", "researcher": {"href": "https://publications.scilifelab.se/researcher/654d5a7904694d2dbeb00f4dc718fe99.json"}}, {"family": "Kobe", "given": "B", "initials": "B", "orcid": "0000-0001-9413-9166", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7de23cf90764ba5a38892c47ca042cc.json"}}, {"family": "Xu", "given": "H", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Nanson", "given": "J D", "initials": "JD", "orcid": "0000-0003-1306-1948", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee17f582fbf049118c7e4709fdbff822.json"}}], "type": "journal article", "published": "2024-09-01", "journal": {"title": "Acta Crystallogr D Struct Biol", "issn": "2059-7983", "volume": "80", "issue": "Pt 9", "pages": "699-712", "issn-l": "2059-7983"}, "abstract": "Eukaryotic TIR (Toll/interleukin-1 receptor protein) domains signal via TIR-TIR interactions, either by self-association or by interaction with other TIR domains. In mammals, TIR domains are found in Toll-like receptors (TLRs) and cytoplasmic adaptor proteins involved in pro-inflammatory signaling. Previous work revealed that the MAL TIR domain (MALTIR) nucleates the assembly of MyD88TIR into crystalline arrays in vitro. A microcrystal electron diffraction (MicroED) structure of the MyD88TIR assembly has previously been solved, revealing a two-stranded higher-order assembly of TIR domains. In this work, it is demonstrated that the TIR domain of TLR2, which is reported to signal as a heterodimer with either TLR1 or TLR6, induces the formation of crystalline higher-order assemblies of MyD88TIR in vitro, whereas TLR1TIR and TLR6TIR do not. Using an improved data-collection protocol, the MicroED structure of TLR2TIR-induced MyD88TIR microcrystals was determined at a higher resolution (2.85 \u00c5) and with higher completeness (89%) compared with the previous structure of the MALTIR-induced MyD88TIR assembly. Both assemblies exhibit conformational differences in several areas that are important for signaling (for example the BB loop and CD loop) compared with their monomeric structures. These data suggest that TLR2TIR and MALTIR interact with MyD88 in an analogous manner during signaling, nucleating MyD88TIR assemblies unidirectionally.", "doi": "10.1107/S2059798324008210", "pmid": "39268708", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11394124"}, {"db": "pii", "key": "S2059798324008210"}], "notes": [], "created": "2024-11-15T13:42:00.132Z", "modified": "2024-11-15T13:42:00.492Z"}, {"entity": "publication", "iuid": "a9d191eeacbf4b7b94a4e1366b774166", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9d191eeacbf4b7b94a4e1366b774166.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9d191eeacbf4b7b94a4e1366b774166"}}, "title": "Using RELION software within the Scipion framework.", "authors": [{"family": "Sharov", "given": "Grigory", "initials": "G", "orcid": "0000-0002-6930-4999", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3cd747674414ac1a94650c94d77cac6.json"}}, {"family": "Morado", "given": "Dustin R", "initials": "DR", "orcid": "0000-0003-4693-3220", "researcher": {"href": "https://publications.scilifelab.se/researcher/eef09b7a95b64a699900bae6a5390e31.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"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"}}], "type": "journal article", "published": "2021-04-01", "journal": {"title": "Acta Crystallogr D Struct Biol", "issn": "2059-7983", "issn-l": "2059-7983", "volume": "77", "issue": "4", "pages": "403-410"}, "abstract": "Scipion is a modular image-processing framework that integrates several software packages under a unified interface while taking care of file formats and conversions. Here, new developments and capabilities of the Scipion plugin for the widely used RELION software package are presented and illustrated with an image-processing pipeline for published data. The user interfaces of Scipion and RELION are compared and the key differences are highlighted, allowing this manuscript to be used as a guide for both new and experienced users of this software. Different on-the-fly image-processing options are also discussed, demonstrating the flexibility of the Scipion framework.", "doi": "10.1107/S2059798321001856", "pmid": "33825701", "labels": {"Cryo-EM": "Technology development"}, "xrefs": [{"db": "pii", "key": "S2059798321001856"}, {"db": "pmc", "key": "PMC8025880"}], "notes": [], "created": "2021-05-19T22:52:58.831Z", "modified": "2023-12-04T10:06:15.737Z"}, {"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": "1ce032b1771744128a78cdd029bd2371", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ce032b1771744128a78cdd029bd2371.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ce032b1771744128a78cdd029bd2371"}}, "title": "Structures of two fimbrial adhesins, AtfE and UcaD, from the uropathogen Proteus mirabilis.", "authors": [{"family": "Jiang", "given": "Wangshu", "initials": "W"}, {"family": "Ubhayasekera", "given": "Wimal", "initials": "W"}, {"family": "Pearson", "given": "Melanie M", "initials": "MM", "orcid": "0000-0003-4553-3276", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c675562ba474fdb81810f9fec308fe6.json"}}, {"family": "Knight", "given": "Stefan D", "initials": "SD", "orcid": "0000-0002-7180-8758", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e9971d1ebb542a8b54601675c3869f5.json"}}], "type": "journal article", "published": "2018-11-01", "journal": {"title": "Acta Crystallogr D Struct Biol", "issn": "2059-7983", "volume": "74", "issue": "Pt 11", "pages": "1053-1062", "issn-l": "2059-7983"}, "abstract": "The important uropathogen Proteus mirabilis encodes a record number of chaperone/usher-pathway adhesive fimbriae. Such fimbriae, which are used for adhesion to cell surfaces/tissues and for biofilm formation, are typically important virulence factors in bacterial pathogenesis. Here, the structures of the receptor-binding domains of the tip-located two-domain adhesins UcaD (1.5 \u00c5 resolution) and AtfE (1.58 \u00c5 resolution) from two P. mirabilis fimbriae (UCA/NAF and ATF) are presented. The structures of UcaD and AtfE are both similar to the F17G type of tip-located fimbrial receptor-binding domains, and the structures are very similar despite having only limited sequence similarity. These structures represent an important step towards a molecular-level understanding of P. mirabilis fimbrial adhesins and their roles in the complex pathogenesis of urinary-tract infections.", "doi": "10.1107/S2059798318012391", "pmid": "30387764", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pii", "key": "S2059798318012391"}], "notes": [], "created": "2024-04-03T14:36:45.656Z", "modified": "2024-04-03T14:36:45.672Z"}, {"entity": "publication", "iuid": "934437159dbf4d53b8a0a4ae01008efb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/934437159dbf4d53b8a0a4ae01008efb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/934437159dbf4d53b8a0a4ae01008efb"}}, "title": "Novel mode of inhibition by D-tagatose 6-phosphate through a Heyns rearrangement in the active site of transaldolase B variants.", "authors": [{"family": "Stellmacher", "given": "Lena", "initials": "L"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Schneider", "given": "Sarah", "initials": "S"}, {"family": "Schneider", "given": "Gunter", "initials": "G"}, {"family": "Sprenger", "given": "Georg A", "initials": "GA"}, {"family": "Samland", "given": "Anne K", "initials": "AK"}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "72", "issn": "2059-7983", "issue": "Pt 4", "pages": "467-476", "title": "Acta Crystallogr D Struct Biol", "issn-l": "2059-7983"}, "abstract": "Transaldolase B (TalB) and D-fructose-6-phosphate aldolase A (FSAA) from Escherichia coli are C-C bond-forming enzymes. Using kinetic inhibition studies and mass spectrometry, it is shown that enzyme variants of FSAA and TalB that exhibit D-fructose-6-phosphate aldolase activity are inhibited covalently and irreversibly by D-tagatose 6-phosphate (D-T6P), whereas no inhibition was observed for wild-type transaldolase B from E. coli. The crystal structure of the variant TalB(F178Y) with bound sugar phosphate was solved to a resolution of 1.46 \u00c5 and revealed a novel mode of covalent inhibition. The sugar is bound covalently via its C2 atom to the \u2107-NH2 group of the active-site residue Lys132. It is neither bound in the open-chain form nor as the closed-ring form of D-T6P, but has been converted to \u03b2-D-galactofuranose 6-phosphate (D-G6P), a five-membered ring structure. The furanose ring of the covalent adduct is formed via a Heyns rearrangement and subsequent hemiacetal formation. This reaction is facilitated by Tyr178, which is proposed to act as acid-base catalyst. The crystal structure of the inhibitor complex is compared with the structure of the Schiff-base intermediate of TalB(E96Q) formed with the substrate D-fructose 6-phosphate determined to a resolution of 2.20\u2005\u00c5. This comparison highlights the differences in stereochemistry at the C4 atom of the ligand as an essential determinant for the formation of the inhibitor adduct in the active site of the enzyme.", "doi": "10.1107/S2059798316001170", "pmid": "27050126", "labels": {"Protein Science Facility (PSF)": "Service"}, "xrefs": [{"db": "pii", "key": "S2059798316001170"}], "notes": [], "created": "2017-05-03T13:02:44.457Z", "modified": "2017-09-06T11:42:09.191Z"}], "created": "2017-05-09T09:12:06.493Z", "modified": "2020-11-27T13:14:09.022Z"}