Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution

Schluenzen, Frank; Tocilj, Ante; Zarivach, Raz; Harms, Joerg; Gluehmann, Marco; Janell, Daniela; Bashan, Anat; Bartels, Heike; Agmon, Ilana; Franceschi, François; Yonath, Ada

doi:10.1016/s0092-8674(00)00084-2

Cited by 930 publications

(740 citation statements)

References 64 publications

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“…Early structures included myoglobin (1 PDB ID 1mbn [6,7]), the first structure solved by X-ray crystallography, and small enzymes (2 top 4pti [48], bottom right 2cha [49], bottom left 3cpa [50]). As technologies developed, the archive grew to host examples of tRNA (3 6tna [51]), viruses (4 4rhv [52]), antibodies (5 1igt [53]), protein-DNA complexes (6 top to bottom, 1gdt [54], 1tro [55], 2bop [56], 1aoi [57]), ribosomes (7 1fjg, 1fka, 1ffk [58][59][60]), and chaperones (8 1aon [61])…”

Section: Validationmentioning

confidence: 99%

The Protein Data Bank archive as an open data resource

Berman

Kleywegt

Nakamura

et al. 2014

J Comput Aided Mol Des

117

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Section: Validationmentioning

confidence: 99%

The Protein Data Bank archive as an open data resource

Berman

Kleywegt

Nakamura

et al. 2014

J Comput Aided Mol Des

117

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show abstract

“…Even after the revolution in information content provided by the ribosome structures (Ban et al 2000;Schluenzen et al 2000;Wimberley et al 2000), most RNA backbone analyses have depended on some form of simplification: on plots for pairs of dihedrals (Kim et al 1973;Murthy et al 1999), on reduced dimensionality methods (Sims and Kim 2003), or on use of few parameters insensitive to the most common errors, such as the h,u virtual-angle system (Malathi and Yathindra 1980;Olson 1980;Duarte and Pyle 1998;Wadley and Pyle 2004), which is still the method most often used for identifying or comparing backbone motifs in an unfiltered general database.…”

Section: Introductionmentioning

confidence: 99%

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

Richardson

Schneider²,

Murray³

et al. 2008

RNA

235

438

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A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a qualityfiltered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle dezabgd combinations empirically found favorable for the sugar-to-sugar ''suite'' unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for dez and a lowercase letter for abgd, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs.

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“…Studies into the composition and structure of prokaryotic ribosomes have been long-time undertakings and have culminated recently with high-resolution structures for bacterial (Schluenzen et al, 2000;Wimberly et al, 2000;Harms et al, 2001) and archeal (Ban et al, 2000) ribosomal subunits.…”

Section: Introductionmentioning

confidence: 99%

High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome

et al. 2005

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Proteomic studies have addressed the composition of plant chloroplast ribosomes and 70S ribosomes from the unicellular organism Chlamydomonas reinhardtii, but comprehensive characterization of cytoplasmic 80S ribosomes from higher plants has been lacking. We have used two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) to analyse the cytoplasmic 80S ribosomes from the model flowering plant Arabidopsis thaliana. Of the 80 ribosomal protein families predicted to comprise the cytoplasmic 80S ribosome, we have confirmed the presence of 61; specifically, 27 (84%) of the small 40S subunit and 34 (71%) of the large 60S subunit. Nearly half (45%) of the ribosomal proteins identified are represented by two or more distinct spots in the 2-DE gel indicating that these proteins are either post-translationally modified or present as different isoforms. Consistently, MS-based protein identification revealed that at least one-third (34%) of the identified ribosomal protein families showed expression of two or more family members. In addition, we have identified a number of non-ribosomal proteins that co-migrate with the plant 80S ribosomes during gradient centrifugation suggesting their possible association with the 80S ribosomes. Among them, RACK1 has recently been proposed to be a ribosome-associated protein that promotes efficient translation in yeast. The study, thus provides the basis for further investigation into the function of the other identified non-ribosomal proteins as well as the biological meaning of the various ribosomal protein isoforms.

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Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution

Cited by 930 publications

References 64 publications

The Protein Data Bank archive as an open data resource

The Protein Data Bank archive as an open data resource

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome

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