{"entity": "researcher", "timestamp": "2026-08-11T14:03:17.230Z", "family": "Larsson", "given": "Daniel S D", "initials": "DSD", "orcid": "0000-0001-7683-6419", "affiliations": ["Department of Cell and Molecular Biology, Uppsala University, SE 751 24 Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/9e2b9321c1064208b9c0a1b11dde571d.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/9e2b9321c1064208b9c0a1b11dde571d"}}, "publications": [{"entity": "publication", "iuid": "366b9dcbbd5948908195760c17d29905", "links": {"self": {"href": "https://publications.scilifelab.se/publication/366b9dcbbd5948908195760c17d29905.json"}, "display": {"href": "https://publications.scilifelab.se/publication/366b9dcbbd5948908195760c17d29905"}}, "title": "Doublet decoding of tRNASer3 demonstrates plasticity of ribosomal decoding center.", "authors": [{"family": "Krishnaswamy", "given": "Shruthi", "initials": "S", "orcid": "0009-0004-3486-4939", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3419361bb4d468997ff52ecd38dfc51.json"}}, {"family": "Akbar", "given": "Shirin", "initials": "S", "orcid": "0000-0003-2437-9679", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4fff2c547b64e3c81e0c935f911028a.json"}}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD", "orcid": "0000-0001-7683-6419", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e2b9321c1064208b9c0a1b11dde571d.json"}}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Selmer", "given": "Maria", "initials": "M", "orcid": "0000-0001-9079-2774", "researcher": {"href": "https://publications.scilifelab.se/researcher/860221451df4451b8c035ff4cf25c812.json"}}], "type": "journal article", "published": "2025-06-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "5402", "issn-l": "2041-1723"}, "abstract": "Frameshifts can be caused by specific combinations of tRNA and mRNA. The wildtype AGC-decoding E. coli tRNASer3GCU has been shown to induce -1 ribosomal frameshifting on GCA alanine codons, and proposed to read a two-base codon instead of a canonical triplet. However, it has remained unclear whether this type of non-cognate decoding can be accommodated by the ribosome. Here, we perform single-particle cryo-EM reconstructions on E. coli 70S ribosomes with the frameshift-inducing tRNASer3 bound to the non-cognate GCA codon or the cognate AGC codon in the ribosomal A site. The structures demonstrate that doublet decoding is made possible when A1493, the conserved monitoring base in 16S rRNA, mimics a first codon base, forming a Hoogsteen base pair with U36 from the anticodon and stacking with the mRNA. This interaction pushes the first two bases of the A-site codon in position for base pairing with C35 and G34 of the anticodon.", "doi": "10.1038/s41467-025-61016-5", "pmid": "40571681", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12202706"}, {"db": "pii", "key": "10.1038/s41467-025-61016-5"}], "notes": [], "created": "2025-10-29T14:57:32.646Z", "modified": "2025-10-29T14:57:53.989Z"}, {"entity": "publication", "iuid": "d8643fc1bb1a43d3b9fd1f76d1c85fec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d8643fc1bb1a43d3b9fd1f76d1c85fec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d8643fc1bb1a43d3b9fd1f76d1c85fec"}}, "title": "Structural mechanism of FusB-mediated rescue from fusidic acid inhibition of protein synthesis.", "authors": [{"family": "Gonz\u00e1lez-L\u00f3pez", "given": "Adri\u00e1n", "initials": "A", "orcid": "0000-0002-4302-6855", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cdef9bebbf940a5812ce94fa81519e9.json"}}, {"family": "Ge", "given": "Xueliang", "initials": "X", "orcid": "0000-0001-7954-3195", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d0da6ede33c4780ba09400c10b80565.json"}}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD", "orcid": "0000-0001-7683-6419", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e2b9321c1064208b9c0a1b11dde571d.json"}}, {"family": "Sihlbom Wallem", "given": "Carina", "initials": "C"}, {"family": "Sanyal", "given": "Suparna", "initials": "S", "orcid": "0000-0002-7124-792X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5c5ffabce284f28885f6594da1460d6.json"}}, {"family": "Selmer", "given": "Maria", "initials": "M", "orcid": "0000-0001-9079-2774", "researcher": {"href": "https://publications.scilifelab.se/researcher/860221451df4451b8c035ff4cf25c812.json"}}], "type": "journal article", "published": "2025-04-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "3693", "issn-l": "2041-1723"}, "abstract": "The antibiotic resistance protein FusB rescues protein synthesis from inhibition by fusidic acid (FA), which locks elongation factor G (EF-G) to the ribosome after GTP hydrolysis. Here, we present time-resolved single-particle cryo-EM structures explaining the mechanism of FusB-mediated rescue. FusB binds to the FA-trapped EF-G on the ribosome, causing large-scale conformational changes of EF-G that break interactions with the ribosome, tRNA, and mRNA. This leads to dissociation of EF-G from the ribosome, followed by FA release. We also observe two independent binding sites of FusB on the classical-state ribosome, overlapping with the binding site of EF-G to each of the ribosomal subunits, yet not inhibiting tRNA delivery. The affinity of FusB to the ribosome and the concentration of FusB in S. aureus during FusB-mediated resistance support that direct binding of FusB to ribosomes could occur in the cell. Our results reveal an intricate resistance mechanism involving specific interactions of FusB with both EF-G and the ribosome, and a non-canonical release pathway of EF-G.", "doi": "10.1038/s41467-025-58902-3", "pmid": "40251147", "labels": {"Cryo-EM": "Service", "Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12008383"}, {"db": "pii", "key": "10.1038/s41467-025-58902-3"}], "notes": [], "created": "2025-04-24T09:33:19.909Z", "modified": "2025-10-29T14:59:52.946Z"}, {"entity": "publication", "iuid": "23e2b6a4fd7641269a2145e9df329eec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23e2b6a4fd7641269a2145e9df329eec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23e2b6a4fd7641269a2145e9df329eec"}}, "title": "Structures of theStaphylococcus aureusribosome inhibited by fusidic acid and fusidic acid cyclopentane", "authors": [{"family": "Gonz\u00e1lez-L\u00f3pez", "given": "Adri\u00e1n", "initials": "A", "orcid": "0000-0002-4302-6855", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cdef9bebbf940a5812ce94fa81519e9.json"}}, {"family": "Larsson", "given": "Daniel S D", "initials": "DSD", "orcid": "0000-0001-7683-6419", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e2b9321c1064208b9c0a1b11dde571d.json"}}, {"family": "Koripella", "given": "Ravi Kiran", "initials": "RK"}, {"family": "Cain", "given": "Brett N", "initials": "BN"}, {"family": "Chavez", "given": "Martin Garcia", "initials": "MG"}, {"family": "Hergenrother", "given": "Paul J", "initials": "PJ"}, {"family": "Sanyal", "given": "Suparna", "initials": "S", "orcid": "0000-0002-7124-792X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5c5ffabce284f28885f6594da1460d6.json"}}, {"family": "Selmer", "given": "Maria", "initials": "M", "orcid": "0000-0001-9079-2774", "researcher": {"href": "https://publications.scilifelab.se/researcher/860221451df4451b8c035ff4cf25c812.json"}}], "type": "posted-content", "published": "2023-11-20", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2023.11.17.567578", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-27T10:38:38.547Z", "modified": "2025-12-18T19:41:02.048Z"}, {"entity": "publication", "iuid": "c63686240798408489015e6ad1d94744", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c63686240798408489015e6ad1d94744.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c63686240798408489015e6ad1d94744"}}, "title": "Structural Consequences of Deproteinating the 50S Ribosome.", "authors": [{"family": "Larsson", "given": "Daniel S D", "initials": "DSD", "orcid": "0000-0001-7683-6419", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e2b9321c1064208b9c0a1b11dde571d.json"}}, {"family": "Kanchugal P", "given": "Sandesh", "initials": "S"}, {"family": "Selmer", "given": "Maria", "initials": "M", "orcid": "0000-0001-9079-2774", "researcher": {"href": "https://publications.scilifelab.se/researcher/860221451df4451b8c035ff4cf25c812.json"}}], "type": "journal article", "published": "2022-10-31", "journal": {"title": "Biomolecules", "issn": "2218-273X", "volume": "12", "issue": "11", "issn-l": null}, "abstract": "Ribosomes are complex ribonucleoprotein particles. Purified 50S ribosomes subjected to high-salt wash, removing a subset of ribosomal proteins (r-proteins), were shown as competent for in vitro assembly into functional 50S subunits. Here, we used cryo-EM to determine the structures of such LiCl core particles derived from E. coli 50S subunits. A wide range of complexes with large variations in the extent of the ordered 23S rRNA and the occupancy of r-proteins were resolved to between 2.8 \u00c5 and 9 \u00c5 resolution. Many of these particles showed high similarity to in vivo and in vitro assembly intermediates, supporting the inherent stability or metastability of these states. Similar to states in early ribosome assembly, the main class showed an ordered density for the particle base around the exit tunnel, with domain V and the 3'-half of domain IV disordered. In addition, smaller core particles were discovered, where either domain II or IV was unfolded. Our data support a multi-pathway in vitro disassembly process, similar but reverse to assembly. Dependencies between complex tertiary RNA structures and RNA-protein interactions were observed, where protein extensions dissociated before the globular domains. We observed the formation of a non-native RNA structure upon protein dissociation, demonstrating that r-proteins stabilize native RNA structures and prevent non-native interactions also after folding.", "doi": "10.3390/biom12111605", "pmid": "36358955", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9687910"}, {"db": "pii", "key": "biom12111605"}], "notes": [], "created": "2022-11-30T09:47:29.371Z", "modified": "2023-12-04T10:21:17.071Z"}]}