Literature DB >> 11752286

5S Ribosomal RNA Database.

Maciej Szymanski1, Miroslawa Z Barciszewska, Volker A Erdmann, Jan Barciszewski.   

Abstract

Ribosomal 5S RNA (5S rRNA) is an integral component of the large ribosomal subunit in all known organisms with the exception only of mitochondrial ribosomes of fungi and animals. It is thought to enhance protein synthesis by stabilization of a ribosome structure. This paper presents the updated database of 5S rRNA and their genes (5S rDNA). Its short characteristics are presented in the Introduction. The database contains 2280 primary structures of 5S rRNA and 5S rRNA genes. These include 536 eubacterial, 61 archaebacterial, 1611 eukaryotic and 72 organelle sequences. The database is available on line through the World Wide Web at http://biobases.ibch.poznan.pl/5SData/.

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Year:  2002        PMID： 11752286      PMCID： PMC99124          DOI： 10.1093/nar/30.1.176

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  11 in total

1.  Crystal structure of the ribosome at 5.5 A resolution.

Authors:  M M Yusupov; G Z Yusupova; A Baucom; K Lieberman; T N Earnest; J H Cate; H F Noller
Journal:  Science       Date:  2001-03-29       Impact factor: 47.728

2.  Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.

Authors:  M Lu; T A Steitz
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-29       Impact factor: 11.205

3.  Crystallization of engineered Thermus flavus 5S rRNA under earth and microgravity conditions.

Authors:  S Lorenz; M Perbandt; C Lippmann; K Moore; L J DeLucas; C Betzel; V A Erdmann
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-04

Review 4.  Mitochondrial evolution.

Authors:  M W Gray; G Burger; B F Lang
Journal:  Science       Date:  1999-03-05       Impact factor: 47.728

5.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.

Authors:  N Ban; P Nissen; J Hansen; P B Moore; T A Steitz
Journal:  Science       Date:  2000-08-11       Impact factor: 47.728

6.  Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge.

Authors:  Y Xiong; M Sundaralingam
Journal:  RNA       Date:  2000-09       Impact factor: 4.942

7.  The structural basis of ribosome activity in peptide bond synthesis.

Authors:  P Nissen; J Hansen; N Ban; P B Moore; T A Steitz
Journal:  Science       Date:  2000-08-11       Impact factor: 47.728

8.  The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

Authors:  N B Leontis; E Westhof
Journal:  RNA       Date:  1998-09       Impact factor: 4.942

9.  The conformation of loop E of eukaryotic 5S ribosomal RNA.

Authors:  B Wimberly; G Varani; I Tinoco
Journal:  Biochemistry       Date:  1993-02-02       Impact factor: 3.162

10.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors:  J D Thompson; D G Higgins; T J Gibson
Journal:  Nucleic Acids Res       Date:  1994-11-11       Impact factor: 16.971
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  78 in total

1.  Rfam: an RNA family database.

Authors:  Sam Griffiths-Jones; Alex Bateman; Mhairi Marshall; Ajay Khanna; Sean R Eddy
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

Review 2.  5 S rRNA: structure and interactions.

Authors:  Maciej Szymański; Mirosława Z Barciszewska; Volker A Erdmann; Jan Barciszewski
Journal:  Biochem J       Date:  2003-05-01       Impact factor: 3.857

3.  BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences.

Authors:  Rob Knight; Amanda Birmingham; Michael Yarus
Journal:  RNA       Date:  2004-09       Impact factor: 4.942

4.  Evaluation of a sophisticated SCFG design for RNA secondary structure prediction.

Authors:  Markus E Nebel; Anika Scheid
Journal:  Theory Biosci       Date:  2011-12-02       Impact factor: 1.919

5.  Metatranscriptomic analysis of microbes in an Oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation.

Authors:  Shinnosuke Murakami; Kosuke Fujishima; Masaru Tomita; Akio Kanai
Journal:  Appl Environ Microbiol       Date:  2011-12-09       Impact factor: 4.792

6.  Comparing RNA secondary structures using a relaxed base-pair score.

Authors:  Phaedra Agius; Kristin P Bennett; Michael Zuker
Journal:  RNA       Date:  2010-04-01       Impact factor: 4.942

Review 7.  Eukaryotic 5S rRNA biogenesis.

Authors:  Martin Ciganda; Noreen Williams
Journal:  Wiley Interdiscip Rev RNA       Date:  2011-02-25       Impact factor: 9.957

8.  Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA.

Authors:  Eva K Freyhult; Jonathan P Bollback; Paul P Gardner
Journal:  Genome Res       Date:  2006-12-06       Impact factor: 9.043

9.  5S rRNA: Structure and Function from Head to Toe.

Authors:  Jonathan D Dinman
Journal:  Int J Biomed Sci       Date:  2005-06

10.  Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice.

Authors:  Fangqian Ou-Yang; Qing-Jun Luo; Yue Zhang; Casey R Richardson; Yingwen Jiang; Christopher D Rock
Journal:  Funct Integr Genomics       Date:  2013-02-19       Impact factor: 3.410
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