{"entity": "journal", "iuid": "b1fe066bc2524313a853a0b008f9592f", "timestamp": "2026-08-15T13:50:47.876Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Structure.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Structure"}}, "title": "Structure", "issn": "1878-4186", "issn-l": "0969-2126", "publications_count": 10, "publications": [{"entity": "publication", "iuid": "0ded32a86ee84dfba5b29f6592ac8bc5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0ded32a86ee84dfba5b29f6592ac8bc5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0ded32a86ee84dfba5b29f6592ac8bc5"}}, "title": "TRP channels: branching out into the fungal kingdom.", "authors": [{"family": "Hellmich", "given": "Ute A", "initials": "UA"}, {"family": "Delemotte", "given": "Lucie", "initials": "L"}], "type": "journal article", "published": "2022-01-06", "journal": {"title": "Structure", "issn": "1878-4186", "volume": "30", "issue": "1", "pages": "2-4", "issn-l": "0969-2126"}, "abstract": "TRP channels have been heavily pursued as cryo-electron microscopy targets since they rang in the \"resolution revolution.\" Although widespread in eukaryotes, a fungal TRP channel structure was missing. In this issue of Structure, Ahmed et al. (2022) present structural insights into the regulation of yeast TRPY1 by Ca2+ and lipids.", "doi": "10.1016/j.str.2021.12.006", "pmid": "34995478", "labels": {"SciLifeLab Fellow": null, "Lucie Delemotte": null}, "xrefs": [{"db": "pii", "key": "S0969-2126(21)00458-5"}], "notes": [], "created": "2022-12-04T07:15:09.199Z", "modified": "2023-05-15T08:05:52.170Z"}, {"entity": "publication", "iuid": "29b8f565da1a4742bf38227644fc1518", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/29b8f565da1a4742bf38227644fc1518.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/29b8f565da1a4742bf38227644fc1518"}}, "title": "Human NUDT22 Is a UDP-Glucose/Galactose Hydrolase Exhibiting a Unique Structural Fold.", "authors": [{"family": "Carter", "given": "Megan", "initials": "M"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Herr", "given": "Patrick", "initials": "P"}, {"family": "Mart\u00ednez Carranza", "given": "Markel", "initials": "M"}, {"family": "Vallin", "given": "Karl S A", "initials": "KSA"}, {"family": "Throup", "given": "Adam", "initials": "A"}, {"family": "Helleday", "given": "Thomas", "initials": "T"}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P"}], "type": "journal article", "published": "2018-02-06", "journal": {"title": "Structure", "issn": "0969-2126", "volume": "26", "issue": "2", "pages": "295-303.e6", "issn-l": null}, "abstract": "Human NUDT22 belongs to the diverse NUDIX family of proteins, but has, until now, remained uncharacterized. Here we show that human NUDT22 is a Mg", "doi": "10.1016/j.str.2018.01.004", "pmid": "29413322", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S0969-2126(18)30004-2"}], "notes": [], "created": "2018-12-05T12:48:44.026Z", "modified": "2018-12-05T12:48:44.047Z"}, {"entity": "publication", "iuid": "c027e9c3b10f4586b0b591af5062f896", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c027e9c3b10f4586b0b591af5062f896.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c027e9c3b10f4586b0b591af5062f896"}}, "title": "MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.", "authors": [{"family": "Vilas", "given": "Jose Luis", "initials": "JL"}, {"family": "G\u00f3mez-Blanco", "given": "Josu\u00e9", "initials": "J"}, {"family": "Conesa", "given": "Pablo", "initials": "P"}, {"family": "Melero", "given": "Roberto", "initials": "R"}, {"family": "Miguel de la Rosa-Trev\u00edn", "given": "Jos\u00e9", "initials": "J"}, {"family": "Ot\u00f3n", "given": "Joaquin", "initials": "J"}, {"family": "Cuenca", "given": "Jes\u00fas", "initials": "J"}, {"family": "Marabini", "given": "Roberto", "initials": "R"}, {"family": "Carazo", "given": "Jos\u00e9 Mar\u00eda", "initials": "JM"}, {"family": "Vargas", "given": "Javier", "initials": "J"}, {"family": "Sorzano", "given": "Carlos Oscar S", "initials": "COS"}], "type": "journal article", "published": "2018-02-06", "journal": {"title": "Structure", "issn": "0969-2126", "volume": "26", "issue": "2", "pages": "337-344.e4", "issn-l": null}, "abstract": "Since the beginning of electron microscopy, resolution has been a critical parameter. In this article, we propose a fully automatic, accurate method for determining the local resolution of a 3D map (MonoRes). The foundation of this algorithm is an extension of the concept of analytic signal, termed monogenic signal. The map is filtered at different frequencies and the amplitude of the monogenic signal is calculated, after which a criterion is applied to determine the resolution at each voxel. MonoRes is fully automatic without compulsory user parameters, with great accuracy in all tests, and is computationally more rapid than existing methods in the field. In\u00a0addition, MonoRes offers the option of local filtering of the original map based on the calculated local resolution.", "doi": "10.1016/j.str.2017.12.018", "pmid": "29395788", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S0969-2126(17)30443-4"}], "notes": [], "created": "2018-12-05T12:48:40.331Z", "modified": "2018-12-05T12:48:40.351Z"}, {"entity": "publication", "iuid": "f312cb01938443b7b30c4bfdfa6e87da", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f312cb01938443b7b30c4bfdfa6e87da.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f312cb01938443b7b30c4bfdfa6e87da"}}, "title": "The SWI/SNF Subunit INI1 Contains an N-Terminal Winged Helix DNA Binding Domain that Is a Target for Mutations in Schwannomatosis.", "authors": [{"family": "Allen", "given": "Mark D", "initials": "MD"}, {"family": "Freund", "given": "Stefan M V", "initials": "SM"}, {"family": "Zinzalla", "given": "Giovanna", "initials": "G"}, {"family": "Bycroft", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2015-07-07", "journal": {"title": "Structure", "issn": "0969-2126", "volume": "23", "issue": "7", "pages": "1344-1349", "issn-l": null}, "abstract": "SWI/SNF complexes use the energy of ATP hydrolysis to remodel chromatin. In mammals they play a central role in regulating gene expression during differentiation and proliferation. Mutations in SWI/SNF subunits are among the most frequent gene alterations in cancer. The INI1/hSNF5/SMARCB1 subunit is mutated in both malignant rhabdoid tumor, a highly aggressive childhood cancer, and schwannomatosis, a tumor-predisposing syndrome characterized by mostly benign tumors of the CNS. Here, we show that mutations in INI1 that cause schwannomatosis target a hitherto unidentified N-terminal winged helix DNA binding domain that is also present in the BAF45a/PHF10 subunit of the SWI/SNF complex. The domain is structurally related to the SKI/SNO/DAC domain, which is found in a number of metazoan chromatin-associated proteins. ", "doi": "10.1016/j.str.2015.04.021", "pmid": "26073604", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S0969-2126(15)00188-4"}, {"db": "pmc", "key": "PMC4509781"}], "notes": [], "created": "2018-12-05T12:19:23.146Z", "modified": "2018-12-05T12:19:23.167Z"}, {"entity": "publication", "iuid": "cb3d9b91ffa847ae899e2050373dd975", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cb3d9b91ffa847ae899e2050373dd975.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cb3d9b91ffa847ae899e2050373dd975"}}, "title": "Structure-Based Discovery of Selective Serotonin 5-HT 1B Receptor Ligands", "authors": [{"family": "Rodr\u00edguez", "given": "David", "initials": "D"}, {"family": "Brea", "given": "Jos\u00e9", "initials": "J"}, {"family": "Loza", "given": "Mar\u00eda Isabel", "initials": "MI"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}], "type": "journal-article", "published": "2014-08-00", "journal": {"volume": "22", "issn": "0969-2126", "issue": "8", "pages": "1140-1151", "title": "Structure", "issn-l": null}, "abstract": "The development of safe and effective drugs relies on the discovery of selective ligands. Serotonin (5-hydroxytryptamine [5-HT]) G protein-coupled receptors are therapeutic targets for CNS disorders but are also associated with adverse drug effects. The determination of crystal structures for the 5-HT1B and 5-HT2B receptors provided an opportunity to identify subtype selective ligands using structure-based methods. From docking screens of 1.3 million compounds, 22 molecules were predicted to\u00a0be selective for the 5-HT1B receptor over the 5-HT2B subtype, a requirement for safe serotonergic drugs. Nine compounds were experimentally verified as 5-HT1B-selective ligands, with up to 300-fold higher affinities for this subtype. Three of the ligands were agonists of the G protein pathway. Analysis of state-of-the-art homology models of the two 5-HT receptors revealed that the crystal structures were critical for predicting selective ligands. Our results demonstrate that structure-based screening can guide the discovery of ligands with specific selectivity profiles. ", "doi": "10.1016/j.str.2014.05.017", "pmid": "25043551", "labels": {"Affiliated researcher": null, "Jens Carlsson": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:35:04.896Z", "modified": "2022-11-07T11:33:17.542Z"}, {"entity": "publication", "iuid": "d2f02eefc6c24f9fb92dd063b48e3920", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d2f02eefc6c24f9fb92dd063b48e3920.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d2f02eefc6c24f9fb92dd063b48e3920"}}, "title": "Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges", "authors": [{"family": "Kufareva", "given": "Irina", "initials": "I"}, {"family": "Katritch", "given": "Vsevolod", "initials": "V"}, {"family": "Stevens", "given": "Raymond C", "initials": "RC"}, {"family": "Abagyan", "given": "Ruben", "initials": "R"}], "type": "journal-article", "published": "2014-08-00", "journal": {"volume": "22", "issn": "0969-2126", "issue": "8", "pages": "1120-1139", "title": "Structure", "issn-l": null}, "abstract": "Despite tremendous successes of GPCR crystallography, the receptors with available structures represent only a small fraction of human GPCRs. An important role of the modeling community is to maximize structural insights for the remaining receptors and complexes. The community-wide GPCR Dock assessment was established to stimulate and monitor the progress in molecular modeling and ligand docking for GPCRs. The four targets in the present third assessment round presented new and diverse challenges for modelers, including prediction of allosteric ligand interaction and activation states in 5-hydroxytryptamine receptors 1B and 2B, and modeling by extremely distant homology for smoothened receptor. Forty-four modeling groups participated in the assessment. State-of-the-art modeling approaches achieved close-to-experimental accuracy for small rigid orthosteric ligands and models built by close homology, and they correctly predicted protein fold for distant homology targets. Predictions of long loops and GPCR activation states remain unsolved problems.", "doi": "10.1016/j.str.2014.06.012", "pmid": "25066135", "labels": {"Jens Carlsson": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:35:01.517Z", "modified": "2022-11-07T11:33:17.553Z"}, {"entity": "publication", "iuid": "91585eb33d044599840deb1006c93635", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/91585eb33d044599840deb1006c93635.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/91585eb33d044599840deb1006c93635"}}, "title": "Inhibition versus potentiation of ligand-gated ion channels can be altered by a single mutation that moves ligands between intra- and intersubunit sites.", "authors": [{"family": "Br\u00f6mstrup", "given": "Torben", "initials": "T"}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ"}, {"family": "Trudell", "given": "James R", "initials": "JR"}, {"family": "Harris", "given": "R Adron", "initials": "RA"}, {"family": "Lindahl", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2013-08-06", "journal": {"title": "Structure", "issn": "0969-2126", "volume": "21", "issue": "8", "pages": "1307-1316", "issn-l": null}, "abstract": "Pentameric ligand-gated ion channels (pLGICs) are similar in structure but either inhibited or potentiated by alcohols and anesthetics. This dual modulation has previously not been understood, but the determination of X-ray structures of prokaryotic GLIC provides an ideal model system. Here, we show that a single-site mutation at the F14' site in the GLIC transmembrane domain turns desflurane and chloroform from inhibitors to potentiators, and that this is explained by competing allosteric sites. The F14'A mutation opens an intersubunit site lined by N239 (15'), I240 (16'), and Y263. Free energy calculations confirm this site is the preferred binding location for desflurane and chloroform in GLIC F14'A. In contrast, both anesthetics prefer an intrasubunit site in wild-type GLIC. Modulation is therefore the net effect of competitive binding between the intersubunit potentiating site and an intrasubunit inhibitory site. This provides direct evidence for a dual-site model of allosteric regulation of pLGICs. ", "doi": "10.1016/j.str.2013.06.018", "pmid": "23891290", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S0969-2126(13)00241-4"}, {"db": "pmc", "key": "PMC3787718"}, {"db": "mid", "key": "NIHMS502807"}], "notes": [], "created": "2018-12-05T10:00:12.266Z", "modified": "2018-12-05T10:00:12.289Z"}, {"entity": "publication", "iuid": "eb94303f3c24498f85f0bbc2159ba862", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/eb94303f3c24498f85f0bbc2159ba862.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/eb94303f3c24498f85f0bbc2159ba862"}}, "title": "Specific inhibition of caspase-3 by a competitive DARPin: molecular mimicry between native and designed inhibitors.", "authors": [{"family": "Schroeder", "given": "Thilo", "initials": "T"}, {"family": "Barandun", "given": "Jonas", "initials": "J"}, {"family": "Fl\u00fctsch", "given": "Andreas", "initials": "A"}, {"family": "Briand", "given": "Christophe", "initials": "C"}, {"family": "Mittl", "given": "Peer R E", "initials": "PR"}, {"family": "Gr\u00fctter", "given": "Markus G", "initials": "MG"}], "type": "journal article", "published": "2013-02-05", "journal": {"title": "Structure", "issn": "0969-2126", "volume": "21", "issue": "2", "pages": "277-289", "issn-l": null}, "abstract": "Dysregulation of apoptosis is associated with several human diseases. The main apoptotic mediators are caspases, which propagate death signals to downstream targets. Executioner caspase-3 is responsible for the majority of cleavage events and its therapeutic potential is of high interest with to date several available active site peptide inhibitors. These molecules inhibit caspase-3, but also homologous caspases. Here, we describe caspase-3 specific inhibitors D3.4 and D3.8, which have been selected from a library of designed ankyrin repeat proteins (DARPins). The crystal structures of D3.4 and mutants thereof show how high specificity and inhibition is achieved. They also show similarities in the binding mode with that of the natural caspase inhibitor XIAP (X-linked inhibitor of apoptosis). The kinetic data reveal a competitive inhibition mechanism. D3.4 is specific for caspase-3 and does not bind the highly homologous caspase-7. D3.4 therefore is an excellent tool to define the precise role of caspase-3 in the various apoptotic pathways.", "doi": "10.1016/j.str.2012.12.011", "pmid": "23333429", "labels": {"Jonas Barandun": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S0969-2126(12)00466-2"}, {"db": "PDB", "key": "2XZD"}, {"db": "PDB", "key": "2Y0B"}], "notes": [], "created": "2020-09-29T14:05:52.382Z", "modified": "2022-11-07T11:33:32.475Z"}, {"entity": "publication", "iuid": "55874caa884a422fb2e726da3887bf2e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/55874caa884a422fb2e726da3887bf2e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/55874caa884a422fb2e726da3887bf2e"}}, "title": "Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment", "authors": [{"family": "Kufareva", "given": "Irina", "initials": "I"}, {"family": "Rueda", "given": "Manuel", "initials": "M"}, {"family": "Katritch", "given": "Vsevolod", "initials": "V"}, {"family": "Stevens", "given": "Raymond C", "initials": "RC"}, {"family": "Abagyan", "given": "Ruben", "initials": "R"}], "type": "journal-article", "published": "2011-08-00", "journal": {"volume": "19", "issn": "0969-2126", "issue": "8", "pages": "1108-1126", "title": "Structure", "issn-l": null}, "abstract": "The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule antagonists and CXCR4 with a synthetic cyclopeptide. Thirty-five groups submitted their receptor-ligand complex structure predictions prior to the release of the crystallographic coordinates. With closely related homology modeling templates, as for dopamine D3 receptor, and with incorporation of biochemical and QSAR data, modern computational techniques predicted complex details with accuracy approaching experimental. In contrast, CXCR4 complexes that had less-characterized interactions and only distant homology to the known GPCR structures still remained very challenging. The assessment results provide guidance for modeling and crystallographic communities in method development and target selection for further expansion of the structural coverage of the GPCR universe.", "doi": "10.1016/j.str.2011.05.012", "pmid": "21827947", "labels": {"Jens Carlsson": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-03T14:27:42.723Z", "modified": "2022-11-07T11:33:17.675Z"}, {"entity": "publication", "iuid": "eed01589d16047b98de0dc3856a3c431", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/eed01589d16047b98de0dc3856a3c431.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/eed01589d16047b98de0dc3856a3c431"}}, "title": "Plant photosystem I design in the light of evolution.", "authors": [{"family": "Amunts", "given": "Alexey", "initials": "A"}, {"family": "Nelson", "given": "Nathan", "initials": "N"}], "type": "journal article", "published": "2009-05-13", "journal": {"title": "Structure", "issn": "0969-2126", "volume": "17", "issue": "5", "pages": "637-650", "issn-l": null}, "abstract": "Photosystem I (PSI) is a membrane protein complex that catalyzes sunlight-driven transmembrane electron transfer as part of the photosynthetic machinery. Photosynthetic organisms appeared on the Earth about 3.5 billion years ago and provided an essential source of potential energy for the development of life. During the course of evolution, these primordial organisms were phagocytosed by more sophisticated eukaryotic cells, resulting in the evolvement of algae and plants. Despite the extended time interval between primordial cyanobacteria and plants, PSI has retained its fundamental mechanism of sunlight conversion. Being probably the most efficient photoelectric apparatus in nature, PSI operates with a quantum efficiency close to 100%. However, adapting to different ecological niches necessitated structural changes in the PSI design. Based on the recently solved structure of plant PSI, which revealed a complex of 17 protein subunits and 178 prosthetic groups, we analyze the evolutionary development of PSI. In addition, some aspects of PSI structure determination are discussed.", "doi": "10.1016/j.str.2009.03.006", "pmid": "19446520", "labels": {"Alexey Amunts": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S0969-2126(09)00151-8"}], "notes": [], "created": "2020-09-25T14:25:02.796Z", "modified": "2022-11-07T11:30:20.512Z"}], "created": "2018-12-03T14:27:42.736Z", "modified": "2020-11-27T13:12:57.846Z"}