Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge.
Xiong Y
,
Sundaralingam M
.
???displayArticle.abstract???
The crystal structure of r(GCCACCCUG).r(CAGGGUCGGC), helix II of the Xenopus laevis 5S rRNA with a cytosine bulge (underlined), has been determined in two forms at 2.2 A (Form I, space group P4(2)2(1)2, a = b = 57.15 A and c = 43.54 A) and 1.7 A (Form II, space group P4(3)2(1)2, a = b = 32.78 A and c = 102.5 A). The helical regions of the nonamers are found in the standard A-RNA conformations and the two forms have an RMS deviation of 0.75 A. However, the cytosine bulge adopts two significantly different conformations with an RMS deviation of 3.9 A. In Form I, the cytosine bulge forms an intermolecular C+*G.C triple in the major groove of a symmetry-related duplex with intermolecular hydrogen bonds between N4C and O6G, and between protonated N3+C and N7G. In contrast, a minor groove C*G.C triple is formed in Form II with intermolecular hydrogen bonds between O2C and N2G, and between N3C and N3G with a water bridge. A partial major groove opening was observed in Form I structure at the bulge site. Two Ca2+ ions were found in Form I helix whereas there were none in Form II. The structural comparison of these two forms indicates that bulged residues can adopt a variety of conformations with little perturbation to the global helix structure. This suggests that bulged residues could function as flexible latches in bridging double helical motifs and facilitate the folding of large RNA molecules.
Baeyens,
A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing.
1996, Pubmed
Baeyens,
A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing.
1996,
Pubmed
Betzel,
Crystal structure of domain A of Thermus flavus 5S rRNA and the contribution of water molecules to its structure.
1994,
Pubmed
Bhattacharyya,
RNA bulges and the helical periodicity of double-stranded RNA.
1990,
Pubmed
,
Xenbase
Brünger,
Crystallography & NMR system: A new software suite for macromolecular structure determination.
1998,
Pubmed
Cate,
A magnesium ion core at the heart of a ribozyme domain.
1997,
Pubmed
Chang,
A novel neurotoxin, cobrotoxin b, from Naja naja atra (Taiwan cobra) venom: purification, characterization, and gene organization.
1997,
Pubmed
Correll,
Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.
1997,
Pubmed
Dingwall,
HIV-1 tat protein stimulates transcription by binding to a U-rich bulge in the stem of the TAR RNA structure.
1990,
Pubmed
Dokudovskaya,
Loop IV of 5S ribosomal RNA has contacts both to domain II and to domain V of the 23S RNA.
1996,
Pubmed
Ennifar,
The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges.
1999,
Pubmed
Green,
Ribosomes and translation.
1997,
Pubmed
Göringer,
Construction and functional analysis of ribosomal 5S RNA from Escherichia coli with single base changes in the ribosomal protein binding sites.
1986,
Pubmed
Huber,
Nuclease protection analysis of ribonucleoprotein complexes: use of the cytotoxic ribonuclease alpha-sarcin to determine the binding sites for Escherichia coli ribosomal proteins L5, L18, and L25 on 5S rRNA.
1984,
Pubmed
Ippolito,
The structure of the HIV-1 RRE high affinity rev binding site at 1.6 A resolution.
2000,
Pubmed
Ippolito,
A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation.
1998,
Pubmed
Jaffrey,
The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure.
1993,
Pubmed
Jang,
Structure of an RNA internal loop consisting of tandem C-A+ base pairs.
1998,
Pubmed
Joshua-Tor,
Three-dimensional structures of bulge-containing DNA fragments.
1992,
Pubmed
McBryant,
Interaction of the RNA binding fingers of Xenopus transcription factor IIIA with specific regions of 5 S ribosomal RNA.
1995,
Pubmed
,
Xenbase
Meier,
The importance of individual nucleotides for the structure and function of rRNA molecules in E. coli. A mutagenesis study.
1986,
Pubmed
Pan,
Crystal structure of an RNA 16-mer duplex R(GCAGAGUUAAAUCUGC)2 with nonadjacent G(syn).A+(anti) mispairs.
1999,
Pubmed
Pan,
Structure of a 16-mer RNA duplex r(GCAGACUUAAAUCUGC)2 with wobble C.A+ mismatches.
1998,
Pubmed
Parkinson,
New parameters for the refinement of nucleic acid-containing structures.
1996,
Pubmed
Pelham,
A specific transcription factor that can bind either the 5S RNA gene or 5S RNA.
1980,
Pubmed
,
Xenbase
Picard,
Isolation of a 7S particle from Xenopus laevis oocytes: a 5S RNA-protein complex.
1979,
Pubmed
,
Xenbase
Portmann,
The crystal structure of r(CCCCGGGG) in two distinct lattices.
1995,
Pubmed
Portmann,
Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage.
1996,
Pubmed
Pritchard,
Methylphosphonate mapping of phosphate contacts critical for RNA recognition by the human immunodeficiency virus tat and rev proteins.
1994,
Pubmed
ROSSET,
[Apropos of the presence of weak molecular weight RNA in the ribosomes of Escherichia Coli].
1963,
Pubmed
Sergiev,
The environment of 5S rRNA in the ribosome: cross-links to the GTPase-associated area of 23S rRNA.
1998,
Pubmed
Sharp,
Splicing of messenger RNA precursors.
1987,
Pubmed
Shatsky,
Topography of RNA in the ribosome: location of the 3'-end of 5 S RNA on the central protuberance of the 50 S subunit.
1980,
Pubmed
Shi,
The crystal structure of the octamer [r(guauaca)dC]2 with six Watson-Crick base-pairs and two 3' overhang residues.
2000,
Pubmed
Stöffler-Meilicke,
Localization of 3' ends of 5S and 23S rRNAs in reconstituted subunits of Escherichia coli ribosomes.
1981,
Pubmed
Sudarsanakumar,
Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag).
2000,
Pubmed
Szymanski,
5S Ribosomal RNA Data Bank.
1999,
Pubmed
Tang,
Bulge loops used to measure the helical twist of RNA in solution.
1990,
Pubmed
Theunissen,
RNA and DNA binding zinc fingers in Xenopus TFIIIA.
1992,
Pubmed
,
Xenbase
Valegârd,
The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions.
1997,
Pubmed
Wedekind,
Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis.
1999,
Pubmed
Westman,
Removal of t-butyldimethylsilyl protection in RNA-synthesis. Triethylamine trihydrofluoride (TEA, 3HF) is a more reliable alternative to tetrabutylammonium fluoride (TBAF).
1994,
Pubmed
Woese,
Evidence for several higher order structural elements in ribosomal RNA.
1989,
Pubmed
Wu,
Role of a bulged A residue in a specific RNA-protein interaction.
1987,
Pubmed
Xiong,
Crystal structure and conformation of a DNA-RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)-r(GAAGAAGAA).
1998,
Pubmed
Zacharias,
Bulge-induced bends in RNA: quantification by transient electric birefringence.
1995,
Pubmed
Zhang,
Physical studies of 5S RNA variants at position 66.
1989,
Pubmed