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  • proteins
  • Ribosomal RNA must have a strategic and important role that cannot be played by ribosomal proteins, nor perhaps by any other cellular component. (springer.com)
  • The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their amino acid sequences and three-dimensional structures. (ebi.ac.uk)
  • This dissertation evaluated three proteomic workflows in order to successfully characterize the changes in the primary structures of cytoplasmic ribosomal proteins isolated from a mitoxantrone resistant breast cancer cell line that could serve some functional significance to the resistance when compared with a parental drug-susceptible cell line. (umd.edu)
  • The N-terminal ends of 52 of the ribosomal proteins were identified using bottom-up and middle-down mass spectrometric approaches. (umd.edu)
  • Molecular masses and top-down analyses were used to define the alterations in the ribosomal proteins in conjunction with high coverage bottom up and middle-down analyses. (umd.edu)
  • The change in the primary structures of these four ribosomal proteins is believed to alter access to the mRNA tunnel in the ribosome. (umd.edu)
  • Since the C -terminal domain of eukaryotic stalk proteins is involved in specific recognition of elongation factors and some eukaryote-specific RIPs (e.g., trichosanthin and ricin), we postulate that these RIPs may have evolved to hijack the translation-factor-recruiting function of ribosomal stalk in reaching their target site of rRNA. (mdpi.com)
  • An in vitro transcribed and folded ES6 sequence differed from that observed in situ, suggesting that chaperones, ribosomal proteins, and/or the tertiary rRNA interaction could be involved in the in vivo folding of ES6. (diva-portal.org)
  • We find that ribosome biogenesis is a parallel process, that blocks of structured rRNA and proteins assemble cooperatively, and that the entire process is dynamic and can be "re-routed" through different pathways as needed. (pdbj.org)
  • Insights into the origin of the nuclear localization signals in conserved ribosomal proteins. (nih.gov)
  • Eukaryotic ribosomal proteins, unlike their bacterial homologues, possess nuclear localization signals (NLSs) to enter the cell nucleus during ribosome assembly. (nih.gov)
  • Here we provide a comprehensive comparison of bacterial and eukaryotic ribosomes to show that NLSs appear in conserved ribosomal proteins via remodelling of their RNA-binding domains. (nih.gov)
  • This finding enabled us to identify previously unknown NLSs in ribosomal proteins from humans, and suggests that, apart from promoting protein transport, NLSs may facilitate folding of ribosomal RNA. (nih.gov)
  • Different structure of homologous ribosomal proteins within highly conserved rRNA pockets may point to the location of unknown nuclear localization signals.Exemplified by identification of NLS in human ribosomal protein uS12. (nih.gov)
  • Protein uS12 is one of the 15 ribosomal proteins in which extensions have different folds in bacteria and eukaryotes, despite being bound to nearly identical rRNA cavities of bacterial and eukaryotic ribosomes. (nih.gov)
  • Having elucidated previously unknown consensus structural features of NLSs of ribosomal proteins, we next endeavoured to use our structural observations to uncover unknown NLSs. (nih.gov)
  • We preformed structural comparison of all homologous proteins from eukaryotic (S. cerevisiae) and bacterial (E. coli) ribosomes and, where necessary, analysed surrounding of ribosomal proteins in the ribosome structure (Supplementary Online Methods). (nih.gov)
  • In total, we found that 27 out of 32 conserved proteins possess differently folded segments within their rRNA-binding domains between bacteria and eukaryotes, despite overall conserved structure of the adjacent rRNA: in fifteen proteins, seemingly conserved extensions have different fold in bacteria and eukaryotes, and, in seventeen proteins, extensions differ in size despite the high conservation of the surrounding rRNA (Supplementary Fig. 2). (nih.gov)
  • RNAs
  • The structural complexity of the ribosomal RNAs is not merely a gratuitous gesture of nature but is indicative of strong structural and functional roles. (springer.com)
  • anticodon
  • In ribosomal interactions with near-cognate tRNA, deviation from Watson-Crick geometry results in uncompensated desolvation of hydrogen-bonding partners at the codon-anticodon minor groove. (rcsb.org)
  • 1984
  • Van Stolk, B.J., Noller, H.F. (1984) Chemical probing of conformation in large RNA molecules: analysis of 16S ribosomal RNA using diethylpyrocarbonate. (springer.com)
  • tRNA
  • Photochemical cross-linking of unmodified acetyl- valyl-tRNA to 16S RNA at the ribosomal P site. (springer.com)
  • These structures suggest how a modification in the uridine at the wobble position can expand the decoding capability of a tRNA. (rcsb.org)
  • crystal structures
  • Our crystal structures display a significant local distortion of 16S ribosomal RNA induced by streptomycin, including the crucial bases A1492 and A1493 that participate directly in codon recognition. (rcsb.org)
  • Entity
  • This entity is NOT a polypeptide entity and therefore cannot be considered for the all vs. all structure alignments. (rcsb.org)
  • residues
  • Covalent crosslinking of tRNAval1 to 16S RNA at the ribosomal P site: identification of the crosslinked residues. (springer.com)
  • We conclude that in ribosomal RNA's, which are generally G-rich, guanine residues may participate in hitherto unpredicted conformations, some of which may be metastable while others are equilibrium structures. (uni-bielefeld.de)
  • structural
  • For these reasons, it is essential that the structural and functional domains of the ribosomal RNA within the ribosome be clearly defined and mapped. (springer.com)
  • Cryo-EM reconstruction has visualized many ES on the ribosomal surface which have given clues about function and structural features. (diva-portal.org)
  • The PDBFlex database explores the intrinsic flexibility of protein structures by analyzing structural variations of the same protein across the archive. (rcsb.org)
  • The structure of the P. furiosus RP-L35Ae presented in this article constitutes the first structural representative from this protein domain family. (semanticscholar.org)
  • genetic
  • Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. (pdbj.org)
  • Aminoglycoside antibiotics that bind to 30 S ribosomal A-site RNA cause misreading of the genetic code and inhibit translocation. (sciencemag.org)
  • domain
  • We present here the crystal structure of the EntB protein that contains an N-terminal isochorismate lyase domain that functions in the synthesis of 2,3-dihydroxybenzoate and a C-terminal carrier protein domain. (rcsb.org)