{"data":{"id":"10.6084/m9.figshare.1400544","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1400544","prefix":"10.6084","suffix":"m9.figshare.1400544","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Kligun, Efrat","nameType":"Personal","givenName":"Efrat","familyName":"Kligun","affiliation":[],"nameIdentifiers":[]},{"name":"Mandel-Gutfreund, Yael","nameType":"Personal","givenName":"Yael","familyName":"Mandel-Gutfreund","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"The role of RNA conformation in RNA-protein recognition"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2015,"subjects":[{"subject":"Computational Biology"},{"subject":"60506 Virology","subjectScheme":"FOR"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"110309 Infectious Diseases","subjectScheme":"FOR"},{"subject":"FOS: Health sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Health sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Biological Sciences"},{"subject":"Chemistry"},{"subject":"Molecular Biology"},{"subject":"Physics"},{"subject":"Biochemistry"},{"subject":"Biophysics"}],"contributors":[],"dates":[{"date":"2015-05-01","dateType":"Created"},{"date":"2015-12-03","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15476286.2015.1040977","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["793953 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Interactions between protein and RNA play a key role in many biological processes in the gene expression pathway. Those interactions are mediated through a variety of RNA-binding protein domains, among them the highly abundant RNA recognition motif (RRM). Here we studied protein-RNA complexes from different RNA binding domain families solved by NMR and x-ray crystallography. Characterizing the structural properties of the RNA at the binding interfaces revealed an unexpected number of nucleotides with unusual RNA conformations, specifically found in RNA-RRM complexes. Moreover, we observed that the RNA nucleotides that are directly involved in interactions with the RRM domains, via hydrogen bonds and hydrophobic contacts, are significantly enriched with unique RNA conformations. Further examination of the sequences binding the RRM domain showed a preference for G nucleotides in \u003ci\u003esyn\u003c/i\u003e conformation to precede or to follow U nucleotides in the \u003ci\u003eanti\u003c/i\u003e-conformation, and U nucleotides in C2' endo conformation to precede U and G nucleotides possessing the more common C3' endo conformation. These findings imply a possible mode of RNA recognition by the RRM domains which enables the recognition of a wide variety of different RNA sequences and shapes. Overall, this study suggests an additional way by which the RRM domain recognizes its RNA target, involving a conformational readout.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"https://tandf.figshare.com/articles/dataset/The_role_of_RNA_conformation_in_RNA_protein_recognition/1400544","contentUrl":null,"metadataVersion":4,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"viewsOverTime":[],"downloadCount":0,"downloadsOverTime":[],"referenceCount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