• A phylogenetically conserved ribosomal protein L16p/L10e organizes the architecture of the aminoacyl tRNA binding site on the large ribosomal subunit. (rcsb.org)
  • 16S ribosomal RNA (or 16S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA). (wikipedia.org)
  • The bacterial 16S gene contains nine hypervariable regions (V1-V9), ranging from about 30 to 100 base pairs long, that are involved in the secondary structure of the small ribosomal subunit. (wikipedia.org)
  • One example is the conserved bacterial ribosome silencing factor (RsfS) that binds to uL14 protein onto the large ribosomal subunit and prevents its association with the small subunit. (nih.gov)
  • Here we describe the binding mode of Staphylococcus aureus RsfS to the large ribosomal subunit and present a 3.2 Å resolution cryo-EM reconstruction of the 50S-RsfS complex together with the crystal structure of uL14-RsfS complex solved at 2.3 Å resolution. (nih.gov)
  • Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. (embl.de)
  • In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. (embl.de)
  • A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. (embl.de)
  • In starvation conditions, the reinitiating ribosomes bypass uORFs 2-4 and reinitiate at GCN4 instead, owing to lowered availability of the ternary complex (TC)-comprised of initiation factor 2 (eIF2), GTP, and initiator Met-tRNAi-which binds to the small (40S) ribosomal subunit to assemble a 43S preinitiation complex (PIC). (nih.gov)
  • Subsequently, we used the Gcd− selection to identify domains/residues in eIF2 and tRNAi, eIF1, eIF1A, eIF3, and residues of 18S rRNA located near the 'P' decoding site of the 40S subunit, that participate in rapid TC recruitment in vivo (Figure 1A). (nih.gov)
  • Here, we report that mutations of an IRES domain that docks in the 40S subunit's decoding groove cause only a local perturbation in IRES structure and result in conformational changes in the IRES-rabbit 40S subunit complex. (janelia.org)
  • Structure of the thermus thermophilus 30s ribosomal subunit complexed with a valine-asl with cmo5u in position 34 bound to an mrna with a gua-codon in the a-site and paromomycin. (edu.pl)
  • Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal proteins. (wikipedia.org)
  • Most of the proteins interact with multiple RNA elements, often from different domains. (embl.de)
  • In this way proteins serve to organise and stabilise the rRNA tertiary structure. (embl.de)
  • The amino-terminal NG domain of SRP is bound to the ribosomal proteins uL23 and uL29, next to the tunnel exit and the carboxy-terminal M domain to the ribosomal 23S RNA 6 . (nature.com)
  • The achievement, reported in Cell , reveals in unprecedented detail how strands of ribonucleic acid (RNA), cellular molecules that are inherently sticky and prone to misfold, are "chaperoned" by ribosomal proteins into folding properly and forming one of the main components of ribosomes. (scripps.edu)
  • Our study indicates that in ribosomal RNA-folding, and perhaps more generally in RNA-folding in cells, many proteins help fold RNA though weak, transient and semi-specific interactions with it," Duss says. (scripps.edu)
  • The matrix exposed C-terminal α-helical domain of Oxa1 can bind mitochondrial ribosomes to facilitate co-translational insertion of proteins into the mitochondrial membrane ( Jia et al . (tcdb.org)
  • Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure. (cam.ac.uk)
  • There is a strong emphasis on the structure of molecules, particularly proteins, which are the nanoscale machines that carry out most processes in living organisms. (bbk.ac.uk)
  • Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. (embl-heidelberg.de)
  • Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands. (embl-heidelberg.de)
  • The domain is named after the von Willebrand factor (VWF) type C repeat which is found in multidomain protein/multifunctional proteins involved in maintaining homeostasis. (embl-heidelberg.de)
  • The presence of this region in a number of other complex-forming proteins points to the possible involvment of the VWFC domain in complex formation. (embl-heidelberg.de)
  • There are 2184 VWC domains in 1039 proteins in SMART's nrdb database. (embl-heidelberg.de)
  • To display all proteins with a VWC domain in a specific node, click on it. (embl-heidelberg.de)
  • The complete taxonomic breakdown of all proteins with VWC domain is also avaliable . (embl-heidelberg.de)
  • This domain occurred 3 times on human genes ( 6 proteins). (umbc.edu)
  • In case of proteins for which it is possible to identify the secondary structure, symbols are given in the Stride classification (e.g. (edu.pl)
  • Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. (janelia.org)
  • Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. (janelia.org)
  • Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA and ribosomal proteins have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy. (ox.ac.uk)
  • also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. (ox.ac.uk)
  • ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. (ox.ac.uk)
  • Crystal structure of the bacterial ribosome from escherichia coli in complex with the antibiotic kasugamyin at 3.5A resolution. (berkeley.edu)
  • Ramakrishnan, V. Ribosome structure and the mechanism of translation. (nature.com)
  • The work provided a detailed look at a complex, and until-now mysterious, part of E. coli ribosome assembly-the formation of an entire major component, or domain, of the E. coli ribosome, with assistance from eight protein partners that end up incorporated into the structure. (scripps.edu)
  • The ribosome-NC contacts within the vestibule define these NC pathways and modulate position of a folded immunoglobulin domain outside the ribosome. (biorxiv.org)
  • Ribosome-nascent chain complexes (RNCs) studied by cryo-EM provided us with "snapshots" of most-stable states of NCs within the ribosomal tunnel 9-13. (biorxiv.org)
  • RNCs comprising the fifth and sixth domains of ABP-120 filamin protein (referred below as FLN5 and FLN6) have been analysed by NMR spectroscopy in the vicinity of the ribosome 17,18,19. (biorxiv.org)
  • In these RNCs, the FLN5 domain is tethered to the ribosome via different length sequences from FLN6 domain ( Fig. 1a ). (biorxiv.org)
  • The former but not the latter has a ribosome binding domain ( Preuss et al . (tcdb.org)
  • Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicable to model RNAs, which are readily crystallized and often give rise to higher resolution crystal structures suitable for detailed analysis of ligand-RNA interactions. (escholarship.org)
  • The ability of the HCV IRES to manipulate the ribosome provides insight into how the ribosome's structure and function can be altered by bound RNAs, including those derived from cellular invaders. (janelia.org)
  • Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family. (rostlab.org)
  • Here we report the structure of a bacterial nitrate/nitrite transport protein, NarK, from Escherichia coli, with and without substrate. (janelia.org)
  • In Escherichia coli, a proportion of the PNPase is recruited into a multi-enzyme assembly, known as the RNA degradosome, through an interaction with the scaffolding domain of the endoribonuclease RNase E. Here, we report crystal structures of E. coli PNPase complexed with the recognition site from RNase E and with manganese in the presence or in the absence of modified RNA. (port.ac.uk)
  • Background: Ribosomal protein S15 is a primary RNA-binding protein that binds to the central domain of 16S rRNA. (caltech.edu)
  • Ribosomal protein L31e, which is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel. (embl.de)
  • The RNA binding domain of ribosomal protein L11: three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA. (expasy.org)
  • These types of RNA are transfer RNA (tRNA), ribosomal RNA (rRNA), and messenger RNA (mRNA). (databasefootball.com)
  • 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. (frontiersin.org)
  • Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis. (frontiersin.org)
  • The biosynthesis of the glycopeptide antibiotics, of which teicoplanin and vancomycin are representative members, relies on the combination of non-ribosomal peptide synthesis and modification of the peptide by cytochrome P450 (Oxy) enzymes while the peptide remains bound to the peptide synthesis machinery. (rcsb.org)
  • We have structurally characterized the final peptidyl carrier protein domain of the teicoplanin non-ribosomal peptide synthetase machinery: this domain is believed to mediate the interactions with tailoring Oxy enzymes in addition to its function as a shuttle for intermediates between multiple non-ribosomal peptide synthetase domains. (rcsb.org)
  • The structures exhibit the same general fold as the majority of known carrier protein structures, in spite of the complex biosynthetic role that PCP domains from the final non-ribosomal peptide synthetase module must play in glycopeptide antibiotic biosynthesis. (rcsb.org)
  • These structures thus support the hypothesis that it is subtle rearrangements, rather than dramatic conformational changes, which govern carrier protein interactions and selectivity during non-ribosomal peptide synthesis. (rcsb.org)
  • Zavialov, A. V., Buckingham, R. H. & Ehrenberg, M. A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. (nature.com)
  • the entire crystal structure contains two 70s ribosomes and is described in remark 400. (berkeley.edu)
  • He shared the 2009 Nobel Prize in Chemistry with Thomas A. Steitz and Ada Yonath for research on the structure and function of ribosomes . (wikipedia.org)
  • While 16S hypervariable regions can vary dramatically between bacteria, the 16S gene as a whole maintains greater length homogeneity than its eukaryotic counterpart (18S ribosomal RNA), which can make alignments easier. (wikipedia.org)
  • Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. (ox.ac.uk)
  • Its two-layered alpha+beta architecture is significantly similar to those of the archaeal and bacterial homologues, substantiating a high degree of structural conservation across the three phylogenetic domains. (rcsb.org)
  • 2015 . The crystal structure of full-length E. coli YidC revealed that a hydrophilic groove, formed by five transmembrane helices, is a conserved structural feature of YidC, as compared to the previous YidC structure from Bacillus halodurans , which lacks a periplasmic domain. (tcdb.org)
  • High-resolution crystal structure analysis confirmed that the HX RNA is a faithful structural model of the ribosomal target. (escholarship.org)
  • The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans raises questions as to their structural and evolutionary relationships. (ox.ac.uk)
  • With the rapid progress and improvements in the fields of macromolecular crystallography, Cryo-EM, small angle scattering, electron diffraction and use of XFELs, the new LINXS theme INTEGRATIVE STRUCTURAL BIOLOGY is formed to advance cutting-edge research and to encourage new users to utilize integrative structure biology to address key scientific questions. (lu.se)
  • Conclusions: The conformation of the N-terminal α helix is quite different from that reported in a recent NMR structure of S15 from Thermus thermophilus. (caltech.edu)
  • Studies using cryo-EM have shown NC folding within the exit tunnel is largely limited to the formation of rudimentary secondary structure, pre-dominantly α helices within different areas of the tunnel, while β hairpins as well as the formation of small domains in the wider vestibule region of the tunnel 9-13. (biorxiv.org)
  • Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands. (embl-heidelberg.de)
  • KdpD is a four-spanning membrane protein that has two large cytoplasmic domains at the amino- and at the carboxyterminus, respectively. (nature.com)
  • In general, the signal for insertion into the inner bacterial membrane is located in the first hydrophobic transmembrane domain and insertion is catalysed by the Sec translocase and/or YidC insertase. (nature.com)
  • At different stages of the insertion process, conformational changes in YidC's TM domain and membrane core have a mechanistic effect on Pf3 coat protein insertion. (tcdb.org)
  • When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution. (janelia.org)
  • HN - 2008 BX - Lateral Sinus MH - Atrial Septum UI - D054087 MN - A07.541.459.249 MS - The thin membrane-like muscular structure separating the right and the left upper chambers (HEART ATRIA) of a heart. (bvsalud.org)
  • Arkov, A. L. & Murgola, E. J. Ribosomal RNAs in translation termination: facts and hypothesis. (nature.com)
  • It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. (wikipedia.org)
  • RL11_THEMA ] This protein binds directly to 23S ribosomal RNA. (proteopedia.org)
  • While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA. (proteopedia.org)
  • SRP is universally conserved in its core region that consists of a ribonucleoprotein particle, the SRP RNA (4.5S RNA in E. coli ) and the protein component SRP54 (Ffh in E. coli for "fifty-four-homolog") that binds to the conserved RNA domain IV 4 . (nature.com)
  • Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. (frontiersin.org)
  • This involved the transcription, or copying out from its corresponding gene, of a ribosomal RNA, and initial interactions of this RNA strand with a ribosomal protein. (scripps.edu)
  • Similarly, the large ribosomal RNA gene clusters that reside on different chromosomes manage to find each other in almost every cell nucleus to form another easily discernable nuclear entity, the nucleolus [ 27 - 29 ]. (biomedcentral.com)
  • Contains the SH2D1A gene for SH2 domain protein 1A, Duncan's disease (lymphoproliferative syndrome) (DSHP), part of a 60S Acidic Ribosomal protein 1 (RPLP1) LIKE gene and part of a mouse DOC4 LIKE gene. (lu.se)
  • We now provide evidence that two growth-regulated, nucleus- and cytoplasm-localized protein kinases, 90-kDa ribosomal S6 kinase (RSK) and mitogen-activated protein kinase (MAP kinase), contribute to the serum-induced phosphorylation of c-Fos. (nih.gov)
  • Based on a 1.9 Å resolution crystal structure of the C-terminal kinase domain of the mouse p90 Ribosomal S6 Kinase 2 (RSK2) inhibited by DMF we describe a central binding site in RSKs and the closely related Mitogen and Stress-activated Kinases (MSKs). (au.dk)
  • This domain is found in a number of enzymes of known structure as well as in urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis. (embl.de)
  • The phosphorylation sites identified for RSK (Ser-362) and MAP kinase (Ser-374) are in the transrepression domain. (nih.gov)
  • We also made key contributions to identifying the eIF2α kinase Gcn2 and elucidating its regulation by amino acids, via allosteric control of kinase activity by uncharged tRNAs and Gcn2 regulatory domains, and by the TOR pathway through Gcn2-Ser577 phosphorylation. (nih.gov)
  • A key finding was that the ribosomal protein partners guide the folding of the RNA strand through multiple temporary interactions with the strand, well before they nestle into their final places in the folded RNA-protein molecule. (scripps.edu)
  • Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus. (rostlab.org)
  • The structures reveal a positively charged substrate-translocation pathway lacking protonatable residues, suggesting that NarK functions as a nitrate/nitrite exchanger and that protons are unlikely to be co-transported. (janelia.org)
  • Functionally, the mutations decrease IRES activity by inhibiting the first ribosomal translocation event, and modeling results suggest that this effect occurs through an interaction with a single ribosomal protein. (janelia.org)
  • The intermolecular contacts that this α helix makes with a neighboring molecule in the crystal, however, closely resemble the intramolecular contacts that occur in the NMR structure. (caltech.edu)
  • SH2 domain protein 1A (SLAM-associated protein) (T cell signal transduction molecule SAP) (Duncan's disease SH2-protein). (lu.se)
  • Nonetheless, nascent polypeptides with more complex tertiary structure fold close to and outside the tunnel, as found for spectrin - a three-helix bundle protein, and titin, an all beta-sheet immunoglobulin domain 10,13. (biorxiv.org)
  • In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. (frontiersin.org)
  • In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. (frontiersin.org)
  • However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. (frontiersin.org)
  • This finding, previously shown for Bacteria, was as well observed for the archaeal domain. (frontiersin.org)
  • Since then, the contribution of the archaeal domain to ecosystem function and diversity was often underestimated in many research fields and studies. (frontiersin.org)
  • Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. (escholarship.org)
  • Polynucleotide phosphorylase (PNPase) is a processive exoribonuclease that contributes to messenger RNA turnover and quality control of ribosomal RNA precursors in many bacterial species. (port.ac.uk)
  • Although no hypervariable region can accurately classify all bacteria from domain to species, some can reliably predict specific taxonomic levels. (wikipedia.org)
  • The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate-oxidizing species reacts. (ox.ac.uk)
  • 1mms is a 4 chain structure with sequence from Atcc 43589 . (proteopedia.org)
  • SRP at the ribosomal exit tunnel scans a nascent chain for bearing a hydrophobic SRP signal sequence 7 . (nature.com)
  • We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. (proteopedia.org)
  • Ribosomal oxygenases are structurally conserved from prokaryotes to humans. (ox.ac.uk)
  • Seit-Nebi, A., Frolova, L., Justesen, J. & Kisselev, L. Class-1 translation termination factors: invariant GGQ minidomain is essential for release activity and ribosomal binding but not for stop codon recognition. (nature.com)
  • Rearrangements of several ribosomal components further suggest that these elements may actively monitor the emerging NC during translation. (biorxiv.org)
  • SwissProt sequences and OMIM curated human diseases associated with missense mutations within the VWC domain. (embl-heidelberg.de)
  • Using solution state NMR, we have determined structures of this PCP domain in two states, the apo and the post-translationally modified holo state, both of which conform to a four-helix bundle assembly. (rcsb.org)
  • DNA is famous for its "double helix" structure, two intertwining strands with complementary bases. (databasefootball.com)
  • Here, we have investigated the HX RNA construct which contains two adjacent ligand binding regions of helix h44 in 16S ribosomal RNA. (escholarship.org)
  • The nascent chain (NC), emerges into the cellular milieu via the ribosomal exit tunnel, which is an active component that regulates the NC passage. (biorxiv.org)
  • Manganese can substitute for magnesium as an essential co-factor for PNPase catalysis, and our crystal structure of the enzyme in complex with manganese suggests how the metal is positioned to stabilise the transition state. (port.ac.uk)
  • We have determined the 2.5-A crystal structure of the human L10 core domain that corresponds to residues 34-182 of the full-length 214 amino acids. (rcsb.org)
  • The information within the KdpD protein that confers SRP interaction was found in the amino-terminal cytoplasmic domain of KdpD, particularly at residues 22-48. (nature.com)
  • The sites of mutations conferring resistance to thiostrepton and micrococcin line a narrow cleft between the RNA and the N-terminal domain. (proteopedia.org)
  • A number of human diseases arise from mutations in VWA domains. (embl-heidelberg.de)
  • The histograms below the weblogo indicate mutations found on the domain. (umbc.edu)
  • This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). (nature.com)
  • In the new study, the team extended this approach by tracking not only the transcription of a ribosomal RNA but also its real-time folding. (scripps.edu)
  • Results: The crystal structure of S15 from Bacillus stearothermophilus has been solved to 2.1 å resolution. (caltech.edu)
  • Crystal structure of a nitrate/nitrite exchanger. (janelia.org)
  • Solution studies showed that HX RNA carrying a fluorescent 2-aminopurine modification provides a model system that can be used to monitor ligand binding to both the ribosomal decoding site and, through an indirect effect, the hygromycin B interaction region. (escholarship.org)
  • Our group discovered the Gcn2 positive effectors Gcn1 and Gcn20 and the importance of ribosomal Gcn1/Gcn20/Gcn2 regulatory complexes in Gcn2 activation. (nih.gov)
  • Figure 3: Stereo views showing interaction between functional centres on the RC and RF2 domains. (nature.com)
  • A detailed view of a ribosomal active site: the structure of the L11-RNA complex. (proteopedia.org)
  • Wimberly BT, Guymon R, McCutcheon JP, White SW, Ramakrishnan V. A detailed view of a ribosomal active site: the structure of the L11-RNA complex. (proteopedia.org)
  • Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone N(ε)-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases catalysing modifications of translational and transcriptional machinery. (ox.ac.uk)