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Literature DB >> 20562215

A structural database for k-turn motifs in RNA.

Kersten T Schroeder¹, Scott A McPhee, Jonathan Ouellet, David M J Lilley.

Abstract

The kink-turn (k-turn) is a common structural motif in RNA that introduces a tight kink into the helical axis. k-turns play an important architectural role in RNA structures and serve as binding sites for a number of proteins. We have created a database of known and postulated k-turn sequences and three-dimensional (3D) structures, available via the internet. This site provides (1) a database of sequence and structure, as a resource for the RNA community, and (2) a tool to enable the manipulation and comparison of 3D structures where known.

Mesh：

Substances：
RNA

Year: 2010 PMID： 20562215 PMCID： PMC2905746 DOI： 10.1261/rna.2207910

Source DB: PubMed Journal: RNA ISSN： 1355-8382 Impact factor: 4.942

40 in total

1. Functional interaction of a novel 15.5kD [U4/U6.U5] tri-snRNP protein with the 5' stem-loop of U4 snRNA.

Authors: S Nottrott; K Hartmuth; P Fabrizio; H Urlaub; I Vidovic; R Ficner; R Lührmann
Journal: EMBO J Date: 1999-11-01 Impact factor: 11.598

2. Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment.

Authors: I Vidovic; S Nottrott; K Hartmuth; R Lührmann; R Ficner
Journal: Mol Cell Date: 2000-12 Impact factor: 17.970

3. Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea.

Authors: Timofey S Rozhdestvensky; Thean Hock Tang; Inna V Tchirkova; Jürgen Brosius; Jean-Pierre Bachellerie; Alexander Hüttenhofer
Journal: Nucleic Acids Res Date: 2003-02-01 Impact factor: 16.971

4. Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution.

Authors: Tomoko Hamma; Adrian R Ferré-D'Amaré
Journal: Structure Date: 2004-05 Impact factor: 5.006

5. Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements.

Authors: Anna K Woźniak; Stephanie Nottrott; Eva Kühn-Hölsken; Gunnar F Schröder; Helmut Grubmüller; Reinhard Lührmann; Claus A M Seidel; Filipp Oesterhelt
Journal: RNA Date: 2005-10 Impact factor: 4.942

6. RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics.

Authors: Filip Rázga; Martin Zacharias; Kamila Réblová; Jaroslav Koca; Jirí Sponer
Journal: Structure Date: 2006-05 Impact factor: 5.006

7. Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot.

Authors: Benoit Heppell; Daniel A Lafontaine
Journal: Biochemistry Date: 2008-01-19 Impact factor: 3.162

8. A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?

Authors: E V Koonin; P Bork; C Sander
Journal: Nucleic Acids Res Date: 1994-06-11 Impact factor: 16.971

9. A toolkit for publishing enhanced figures.

Authors: Brian McMahon; Robert M Hanson
Journal: J Appl Crystallogr Date: 2008-07-01 Impact factor: 3.304

10. Induced fit of RNA on binding the L7Ae protein to the kink-turn motif.

Authors: Ben Turner; Sonya E Melcher; Timothy J Wilson; David G Norman; David M J Lilley
Journal: RNA Date: 2005-06-29 Impact factor: 4.942

45 in total

1. Structure and folding of a rare, natural kink turn in RNA with an AA pair at the 2b2n position.

Authors: Kersten T Schroeder; Peter Daldrop; Scott A McPhee; David M J Lilley
Journal: RNA Date: 2012-04-26 Impact factor: 4.942

2. RNA nanotechnology for computer design and in vivo computation.

Authors: Meikang Qiu; Emil Khisamutdinov; Zhengyi Zhao; Cheryl Pan; Jeong-Woo Choi; Neocles B Leontis; Peixuan Guo
Journal: Philos Trans A Math Phys Eng Sci Date: 2013-09-02 Impact factor: 4.226

3. Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction.

Authors: Cigdem Sevim Bayrak; Namhee Kim; Tamar Schlick
Journal: Nucleic Acids Res Date: 2017-05-19 Impact factor: 16.971

Review 4. C/D-box snoRNAs form methylating and non-methylating ribonucleoprotein complexes: Old dogs show new tricks.

Authors: Marina Falaleeva; Justin R Welden; Marilyn J Duncan; Stefan Stamm
Journal: Bioessays Date: 2017-05-15 Impact factor: 4.345

Review 5. Uniqueness, advantages, challenges, solutions, and perspectives in therapeutics applying RNA nanotechnology.

Authors: Peixuan Guo; Farzin Haque; Brent Hallahan; Randall Reif; Hui Li
Journal: Nucleic Acid Ther Date: 2012-08 Impact factor: 5.486

Review 6. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Authors: Jiří Šponer; Giovanni Bussi; Miroslav Krepl; Pavel Banáš; Sandro Bottaro; Richard A Cunha; Alejandro Gil-Ley; Giovanni Pinamonti; Simón Poblete; Petr Jurečka; Nils G Walter; Michal Otyepka
Journal: Chem Rev Date: 2018-01-03 Impact factor: 60.622

7. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches.

Authors: Nathan J Baird; Adrian R Ferré-D'Amaré
Journal: RNA Date: 2012-12-17 Impact factor: 4.942

8. Differentiation and phylogenetic relationships in Mycobacterium spp with special reference to the RNase P RNA gene rnpB.

Authors: Björn Herrmann; Pelle Stolt; Guma Abdeldaim; Carl-Johan Rubin; Leif A Kirsebom; Mikael Thollesson
Journal: Curr Microbiol Date: 2014-06-25 Impact factor: 2.188

Review 9. The GA-minor submotif as a case study of RNA modularity, prediction, and design.

Authors: Wade W Grabow; Zhuoyun Zhuang; Joan-Emma Shea; Luc Jaeger
Journal: Wiley Interdiscip Rev RNA Date: 2013-02-01 Impact factor: 9.957

Review 10. Ultrastable pRNA hexameric ring gearing hexameric phi29 DNA-packaging motor by revolving without rotating and coiling.

Authors: Chad Schwartz; Peixuan Guo
Journal: Curr Opin Biotechnol Date: 2013-05-14 Impact factor: 9.740